![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 days ago
Last modified 8 days ago
#20291 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001ffe04840 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, PIL._imaging, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 51)
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 100838000-10083c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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"name" : "numpy_formathandler.cpython-311-darwin.so"
},
{
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"uuid" : "5bd21324-288d-31d8-a98b-f8c1776ff590",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
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{
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"uuid" : "322fc538-890c-37d6-b941-662f1083ca42",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
"name" : "_version.cpython-311-darwin.so"
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{
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"uuid" : "83f39565-33c4-320a-ac75-81b90af76e46",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
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{
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"uuid" : "bef79d77-164b-32c8-b975-670434b8d743",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
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{
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"uuid" : "4054e3d0-2474-37de-901e-4c10afdac686",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
},
{
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"uuid" : "f660af98-8bcc-35ff-a0a7-91590a2716eb",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_csv.cpython-311-darwin.so",
"name" : "_csv.cpython-311-darwin.so"
},
{
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"uuid" : "0d5e2b04-5266-3fcf-8917-51cab65a30b4",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
},
{
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"uuid" : "6159a840-3c3a-3d9e-9af1-35dea6d209e4",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
},
{
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"uuid" : "bdbfbc59-c41d-3a69-8112-739716f2e836",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
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{
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"uuid" : "06082bf4-58c8-3f16-9f71-841cf9880fbe",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
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"uuid" : "63b5bd02-9626-3588-a39c-88d4f882312b",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
{
"source" : "P",
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"base" : 14006747136,
"size" : 32768,
"uuid" : "7c43df7b-5e3e-3a91-9bc6-b8f9ebd02ec2",
"path" : "\/Applications\/ChimeraX-1.11.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
},
{
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
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{
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"uuid" : "642faf7a-874e-37e6-8aba-2b0cc09a3025",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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{
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"uuid" : "92699527-645f-3d8d-aed8-1cfb0c034e15",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
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"base" : 6816559104,
"size" : 32748,
"uuid" : "984d08b8-f85c-36f5-9e17-5bff7fc779a3",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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{
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"name" : "CoreFoundation",
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{
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"size" : 14974976,
"uuid" : "16d282d0-8b48-3e76-8036-fcb45dece518",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3302.1.400"
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{
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{
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REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 2
Activity Tracing 256K 1
CG image 384K 20
ColorSync 640K 32
CoreAnimation 1776K 111
CoreGraphics 64K 4
CoreGraphics (reserved) 16K 1 reserved VM address space (unallocated)
CoreUI image data 5232K 48
Foundation 48K 2
Kernel Alloc Once 32K 1
MALLOC 4.6G 137
MALLOC guard page 288K 18
Mach message 64K 3
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 768K 48
Stack 198.1M 49
Stack Guard 56.0M 1
VM_ALLOCATE 302.5M 125
VM_ALLOCATE (reserved) 288.0M 3 reserved VM address space (unallocated)
__AUTH 5284K 672
__AUTH_CONST 70.5M 920
__CTF 824 1
__DATA 32.5M 1037
__DATA_CONST 50.5M 1056
__DATA_DIRTY 2763K 342
__FONT_DATA 2352 1
__GLSLBUILTINS 5174K 1
__INFO_FILTER 8 1
__LINKEDIT 637.0M 130
__OBJC_RW 2374K 1
__TEXT 1.3G 1076
__TPRO_CONST 272K 2
dyld private memory 48K 2
mapped file 296.6M 59
owned unmapped memory 87.2M 1
page table in kernel 2868K 1
shared memory 3152K 22
=========== ======= =======
TOTAL 7.9G 5935
TOTAL, minus reserved VM space 7.6G 5935
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},
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===== Log before crash start =====
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow5.cxs"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel
2.08, shown at level 0.185, step 1, values float32
Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel
2.08, shown at level 0.203, step 1, values float32
Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel
2.08, shown at level 0.356, step 1, values float32
Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown
at level 1.17, step 1, values float32
Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel
2.08, shown at level 0.335, step 1, values float32
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown
at level 1.29, step 1, values float32
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel
2.08, shown at level 0.271, step 1, values float32
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32
Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32,
shown at level 1.6, step 1, values float32
Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown
at level 0.649, step 1, values float32
Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown
at level 1.01, step 1, values float32
Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown
at level 0.533, step 1, values float32
Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown
at level 0.567, step 1, values float32
Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831,
shown at level 0.134, step 1, values float32
Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831,
shown at level 0.143, step 1, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 3.78, step 2, values float32
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 3.77, step 2, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at level 3.78, step 1, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at level 3.77, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0602, step 2, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32
Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831,
shown at level 0.0515, step 1, values float32
Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831,
shown at level 8.66, step 1, values float32
Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831,
shown at level 0.0592, step 1, values float32
Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831,
shown at level 9.68, step 1, values float32
Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown
at level 0.612, step 1, values float32
Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown
at level 0.575, step 1, values float32
Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown
at level 1.95, step 1, values float32
Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown
at level 0.569, step 1, values float32
Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown
at level 1.03, step 1, values float32
Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown
at level 0.417, step 1, values float32
Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown
at level 0.487, step 1, values float32
Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown
at level 0.427, step 1, values float32
Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown
at level 0.719, step 1, values float32
Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown
at level 0.525, step 1, values float32
Opened CS_P4_J323_sharp_flip.mrc as #58, grid size 320,320,320, pixel 0.831,
shown at level 0.0616, step 1, values float32
Opened CS_P4_J324_map_locres_flip.mrc as #59, grid size 320,320,320, pixel
0.831, shown at level 3.69, step 1, values float32
Opened CS_P4_J329_sharp_flip.mrc as #60, grid size 320,320,320, pixel 0.831,
shown at level 0.0566, step 1, values float32
Opened CS_P4_J330_locres_flip.mrc as #61, grid size 320,320,320, pixel 0.831,
shown at level 9.71, step 1, values float32
Opened CS_P4_J300_sharp_flip.mrc as #62, grid size 320,320,320, pixel 0.831,
shown at level 0.0575, step 1, values float32
Opened CS_P4_J301_locres_flip.mrc as #63, grid size 320,320,320, pixel 0.831,
shown at level 3.95, step 1, values float32
Log from Thu May 7 21:11:39 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow3.cxs"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel
2.08, shown at level 0.185, step 1, values float32
Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel
2.08, shown at level 0.203, step 1, values float32
Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel
2.08, shown at level 0.356, step 1, values float32
Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown
at level 1.17, step 1, values float32
Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel
2.08, shown at level 0.335, step 1, values float32
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown
at level 1.29, step 1, values float32
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel
2.08, shown at level 0.271, step 1, values float32
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32
Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32,
shown at level 1.6, step 1, values float32
Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown
at level 0.649, step 1, values float32
Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown
at level 1.01, step 1, values float32
Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown
at level 0.533, step 1, values float32
Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown
at level 0.567, step 1, values float32
Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831,
shown at level 0.134, step 1, values float32
Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831,
shown at level 0.143, step 1, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 3.78, step 2, values float32
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 3.77, step 2, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at level 3.78, step 1, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at level 3.77, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0602, step 2, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32
Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831,
shown at level 0.0515, step 1, values float32
Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831,
shown at level 8.66, step 1, values float32
Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831,
shown at level 0.0592, step 1, values float32
Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831,
shown at level 9.68, step 1, values float32
Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown
at level 0.612, step 1, values float32
Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown
at level 0.575, step 1, values float32
Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown
at level 1.95, step 1, values float32
Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown
at level 0.569, step 1, values float32
Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown
at level 1.03, step 1, values float32
Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown
at level 0.417, step 1, values float32
Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown
at level 0.487, step 1, values float32
Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown
at level 0.427, step 1, values float32
Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown
at level 0.719, step 1, values float32
Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown
at level 0.525, step 1, values float32
Opened CS_P4_J323_sharp_flip.mrc as #58, grid size 320,320,320, pixel 0.831,
shown at level 0.0616, step 1, values float32
Opened CS_P4_J324_map_locres_flip.mrc as #59, grid size 320,320,320, pixel
0.831, shown at level 3.69, step 1, values float32
Opened CS_P4_J329_sharp_flip.mrc as #60, grid size 320,320,320, pixel 0.831,
shown at level 0.0566, step 1, values float32
Opened CS_P4_J330_locres_flip.mrc as #61, grid size 320,320,320, pixel 0.831,
shown at level 9.71, step 1, values float32
Log from Thu May 7 15:58:17 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260506_SA-F_B1_workflow.cxs"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel
2.08, shown at level 0.185, step 1, values float32
Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel
2.08, shown at level 0.203, step 1, values float32
Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel
2.08, shown at level 0.356, step 1, values float32
Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown
at level 1.17, step 1, values float32
Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel
2.08, shown at level 0.335, step 1, values float32
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown
at level 1.29, step 1, values float32
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel
2.08, shown at level 0.271, step 1, values float32
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32
Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32,
shown at level 1.6, step 1, values float32
Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown
at level 0.649, step 1, values float32
Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown
at level 1.01, step 1, values float32
Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown
at level 0.533, step 1, values float32
Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown
at level 0.567, step 1, values float32
Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831,
shown at level 0.134, step 1, values float32
Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831,
shown at level 0.143, step 1, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 3.78, step 2, values float32
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 3.77, step 2, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at level 3.78, step 1, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at level 3.77, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0602, step 2, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32
Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831,
shown at level 0.0515, step 1, values float32
Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831,
shown at level 8.66, step 1, values float32
Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831,
shown at level 0.0592, step 1, values float32
Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831,
shown at level 9.68, step 1, values float32
Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown
at level 0.612, step 1, values float32
Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown
at level 0.575, step 1, values float32
Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown
at level 1.95, step 1, values float32
Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown
at level 0.569, step 1, values float32
Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown
at level 1.03, step 1, values float32
Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown
at level 0.417, step 1, values float32
Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown
at level 0.487, step 1, values float32
Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown
at level 0.427, step 1, values float32
Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown
at level 0.719, step 1, values float32
Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown
at level 0.525, step 1, values float32
Log from Wed May 6 15:19:28 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260505_SA-F_B1_workflow.cxs"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel
2.08, shown at level 0.185, step 1, values float32
Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel
2.08, shown at level 0.203, step 1, values float32
Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel
2.08, shown at level 0.356, step 1, values float32
Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown
at level 1.17, step 1, values float32
Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel
2.08, shown at level 0.335, step 1, values float32
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown
at level 1.29, step 1, values float32
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel
2.08, shown at level 0.271, step 1, values float32
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32
Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32,
shown at level 1.6, step 1, values float32
Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown
at level 0.649, step 1, values float32
Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown
at level 1.01, step 1, values float32
Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown
at level 0.533, step 1, values float32
Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown
at level 0.567, step 1, values float32
Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831,
shown at level 0.134, step 1, values float32
Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831,
shown at level 0.143, step 1, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 3.78, step 2, values float32
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 3.77, step 2, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at level 3.78, step 1, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at level 3.77, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0602, step 2, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32
Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831,
shown at level 0.0515, step 1, values float32
Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831,
shown at level 8.66, step 1, values float32
Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831,
shown at level 0.0592, step 1, values float32
Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831,
shown at level 9.68, step 1, values float32
Log from Tue May 5 09:31:57 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow4.cxs"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel
2.08, shown at level 0.185, step 1, values float32
Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel
2.08, shown at level 0.203, step 1, values float32
Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel
2.08, shown at level 0.356, step 1, values float32
Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown
at level 1.17, step 1, values float32
Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel
2.08, shown at level 0.335, step 1, values float32
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown
at level 1.29, step 1, values float32
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel
2.08, shown at level 0.271, step 1, values float32
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32
Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32,
shown at level 1.6, step 1, values float32
Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown
at level 0.649, step 1, values float32
Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown
at level 1.01, step 1, values float32
Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown
at level 0.533, step 1, values float32
Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown
at level 0.567, step 1, values float32
Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831,
shown at level 0.134, step 1, values float32
Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831,
shown at level 0.143, step 1, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 3.78, step 2, values float32
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 3.77, step 2, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at level 3.78, step 1, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at level 3.77, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0602, step 2, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32
Log from Sun May 3 17:29:06 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J216_class_00_00122_volume_sharp.mrc"
Opened cryosparc_P4_J216_class_00_00122_volume_sharp.mrc as #1, grid size
128,128,128, pixel 2.08, shown at level 0.204, step 1, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J216_class_01_00122_volume_sharp.mrc"
Opened cryosparc_P4_J216_class_01_00122_volume_sharp.mrc as #2, grid size
128,128,128, pixel 2.08, shown at level 0.218, step 1, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J216_class_02_00122_volume_sharp.mrc"
Opened cryosparc_P4_J216_class_02_00122_volume_sharp.mrc as #3, grid size
128,128,128, pixel 2.08, shown at level 0.263, step 1, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J216_class_03_00122_volume_sharp.mrc"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.199, step 1, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J216_class_04_00122_volume_sharp.mrc"
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.235, step 1, values float32
> lighting soft
> set bgColor white
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!4 models
> volume #4 level 0.2842
> show #!3 models
> hide #!4 models
> volume #3 level 0.3546
> volume #3 level 0.356
> hide #!3 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!1 models
> color #1 #FCEDFF
> hide #!5 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!1 models
> volume flip #1
Opened cryosparc_P4_J216_class_00_00122_volume_sharp.mrc z flip as #6, grid
size 128,128,128, pixel 2.08, shown at step 1, values float32
> hide #!6 models
> show #!2 models
> volume flip #2
Opened cryosparc_P4_J216_class_01_00122_volume_sharp.mrc z flip as #7, grid
size 128,128,128, pixel 2.08, shown at step 1, values float32
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> volume flip #3
Opened cryosparc_P4_J216_class_02_00122_volume_sharp.mrc z flip as #8, grid
size 128,128,128, pixel 2.08, shown at step 1, values float32
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!8 models
> hide #!5 models
> close #1
> close #2
> close #3
> rename #6 CS_P4_J216_class_0_sharp_flip id #1
> save #1 CS_P4_J216_class_0_sharp_flip.mrc
Cannot determine format for '#1'
> save CS_P4_J216_class_0_sharp_flip.mrc #1
> rename #7 CS_P4_J216_class_1_sharp_flip id #1_sharp_flip.mrc #2
Invalid "id" argument: Expected an integer
> rename #7 CS_P4_J216_class_1_sharp_flip id #1_sharp_flip id #2
Invalid "id" argument: Expected an integer
> rename #7 CS_P4_J216_class_2_sharp_flip id #2
> rename #2 CS_P4_J216_class_1_sharp_flip
> rename #8 CS_P4_J216_class_2_sharp_flip id #3
> save CS_P4_J216_class_1_sharp_flip.mrc #2
> save CS_P4_J216_class_2_sharp_flip.mrc #3
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260430_SA-F_B1_workflow.cxs"
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!5 models
> show #!3 models
> hide #!5 models
> show #!1 models
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-2.4868,0,1,0,6.8233,0,0,1,22.302
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.85834,-0.51214,-0.03115,83.967,-0.50924,-0.85776,0.070198,298.29,-0.06267,-0.044391,-0.99705,270.86
Must specify one map, got 0
> fitmap #1 inMap #3
Fit map CS_P4_J216_class_0_sharp_flip.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 20952 points
correlation = 0.8163, correlation about mean = 0.111, overlap = 1135
steps = 116, shift = 13.1, angle = 14.8 degrees
Position of CS_P4_J216_class_0_sharp_flip.mrc (#1) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.94377261 -0.32509802 0.06003771 31.40521096
-0.32212557 -0.94514622 -0.05416389 308.66342237
0.07435299 0.03177871 -0.99672551 251.62777867
Axis 0.98583616 -0.16420866 0.03409658
Axis point 0.00000000 154.16030965 128.66405805
Rotation angle (degrees) 177.50176084
Shift along axis -11.14516800
> select subtract #1
Nothing selected
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!3 models
> fitmap #2 inMap #3
Fit map CS_P4_J216_class_1_sharp_flip.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 20964 points
correlation = 0.8775, correlation about mean = 0.2387, overlap = 1535
steps = 72, shift = 7.04, angle = 9.35 degrees
Position of CS_P4_J216_class_1_sharp_flip.mrc (#2) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.99017956 0.04949629 -0.13074615 12.42570756
-0.06022022 0.99502365 -0.07938169 18.18421737
0.12616642 0.08647569 0.98823276 -19.36289944
Axis 0.51051058 -0.79077932 -0.33770846
Axis point 165.72686650 0.00000000 88.43510724
Rotation angle (degrees) 9.34870453
Shift along axis -1.49723285
> hide #!2 models
> show #!4 models
> fitmap #4 inMap #3
Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 5887 points
correlation = 0.7186, correlation about mean = 0.04573, overlap = 331.9
steps = 104, shift = 11.1, angle = 13.1 degrees
Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.97455290 -0.13512397 0.17885231 -1.53434267
0.14053006 0.98991548 -0.01785084 -17.74958210
-0.17463660 0.04253071 0.98371398 30.92421506
Axis 0.13349556 0.78151692 0.60943437
Axis point 157.21397711 0.00000000 34.50744362
Rotation angle (degrees) 13.07084305
Shift along axis 4.76985279
> hide #!4 models
> show #!5 models
> select add #5
2 models selected
> view matrix models
> #5,0.70232,-0.70945,-0.058532,142.48,-0.70661,-0.70474,0.063551,312.49,-0.086337,-0.0032735,-0.99626,292.78
> fitmap #5 inMap #3
Fit map cryosparc_P4_J216_class_04_00122_volume_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 20952 points
correlation = 0.896, correlation about mean = 0.3255, overlap = 1903
steps = 100, shift = 4.43, angle = 13 degrees
Position of cryosparc_P4_J216_class_04_00122_volume_sharp.mrc (#5) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.72688934 -0.68457986 0.05461051 119.19907428
-0.67457364 -0.72664609 -0.13013783 337.91149541
0.12877226 0.05775699 -0.98999082 252.38058253
Axis 0.92902840 -0.36668580 0.04947481
Axis point 0.00000000 185.59312596 132.22855036
Rotation angle (degrees) 174.19607958
Shift along axis -0.68154259
> select subtract #5
Nothing selected
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260430_SA-F_B1_workflow.cxs"
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!2 models
> color #2 #FCEDFF
> hide #!2 models
> show #!4 models
> color #4 #FCEDFF
> hide #!4 models
> show #!5 models
> color #5 #FCEDFF
> hide #!5 models
> show #!3 models
> color #5 #E9C29B
> color #5 #FCEDFF
> color #3 #E9C29B
> ui mousemode right translate
> volume #2 level 0.356
> volume #1 level 0.356
> volume #4 level 0.356
> volume #5 level 0.356
> hide #!3 models
> show #!1 models
> undo
[Repeated 1 time(s)]
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.1727
> volume #1 level 0.1851
> show #!2 models
> hide #!1 models
> volume #2 level 0.203
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!4 models
> volume #4 level 0.1532
> show #!3 models
> select add #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.97455,-0.13512,0.17885,1.3208,0.14053,0.98992,-0.017851,-10.868,-0.17464,0.042531,0.98371,31.337
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.085498,-0.64922,0.75578,120.23,0.99605,-0.074063,0.049058,8.8958,0.024125,0.75698,0.65299,-39.323
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.085498,-0.64922,0.75578,134.23,0.99605,-0.074063,0.049058,6.1939,0.024125,0.75698,0.65299,-87.477
> view matrix models
> #4,-0.085498,-0.64922,0.75578,134.33,0.99605,-0.074063,0.049058,6.22,0.024125,0.75698,0.65299,-87.742
> view matrix models
> #4,-0.085498,-0.64922,0.75578,130.4,0.99605,-0.074063,0.049058,5.0583,0.024125,0.75698,0.65299,-76.883
> fitmap #4 inMap #3
Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 42435 points
correlation = 0.7796, correlation about mean = 0.1614, overlap = 1558
steps = 228, shift = 2.07, angle = 23.4 degrees
Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.31733316 -0.35582789 0.87902570 104.58434579
0.93180439 -0.28920783 0.21931579 18.83015631
0.17618244 0.88867618 0.42333722 -81.48445272
Axis 0.41511738 0.43588247 0.79855121
Axis point 65.64014873 66.59534740 0.00000000
Rotation angle (degrees) 126.27076538
Shift along axis -13.44699307
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.85396,0.083596,-0.51358,313.46,-0.52034,-0.13698,0.8429,94.578,0.00011363,0.98704,0.16047,-34.579
> fitmap #4 inMap #3
Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 42435 points
correlation = 0.7628, correlation about mean = 0.1138, overlap = 1507
steps = 160, shift = 8.1, angle = 11.6 degrees
Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.75756109 0.20637267 -0.61928307 295.50473254
-0.63935005 -0.04324082 0.76769900 115.47474727
0.13165378 0.97751755 0.16470194 -51.62941296
Axis 0.18240424 -0.65282152 -0.73522293
Axis point 168.50534676 17.73009752 0.00000000
Rotation angle (degrees) 144.89006320
Shift along axis 16.47604383
> select subtract #4
Nothing selected
> volume #4 level 0.3211
> hide #!3 models
> volume #4 level 0.2347
> volume #4 level 0.2031
> hide #!4 models
> show #!5 models
> volume #5 level 0.1924
> volume #5 level 0.2064
> ui mousemode right translate
> show #!3 models
> hide #!5 models
> color #3 #B9DBD5
> hide #!3 models
> show #!1 models
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> save P4_J216_class_0_sharp.png supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save P4_J216_class_1_sharp.png supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> save P4_J216_class_2_sharp.png supersample 3 transparentBackground true
> hide #!3 models
> show #!4 models
> save P4_J216_class_3_sharp.png supersample 3 transparentBackground true
> hide #!4 models
> show #!5 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> view name P1
[Repeated 1 time(s)]
> save P4_J216_class_0_sharp.png supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save P4_J216_class_1_sharp.png supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> save P4_J216_class_2_sharp.png supersample 3 transparentBackground true
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> save P4_J216_class_3_sharp.png supersample 3 transparentBackground true
> hide #!4 models
> show #!5 models
> vieww P1
Unknown command: vieww P1
> view P1
[Repeated 1 time(s)]
> save P4_J216_class_4_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260430_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J219_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J219_002_volume_map_sharp.mrc as #6, grid size 80,80,80,
pixel 3.32, shown at level 0.854, step 1, values float32
> hide #!5 models
> show #!3 models
> select add #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.50968,-0.8597,0.033732,182.49,-0.85693,-0.50376,0.10903,313.05,-0.076743,-0.084479,-0.99347,263.76
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.50968,-0.8597,0.033732,181.37,-0.85693,-0.50376,0.10903,307.2,-0.076743,-0.084479,-0.99347,286.3
> fitmap #6 inMap #3
Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 5120 points
correlation = 0.7368, correlation about mean = 0.07448, overlap = 1741
steps = 88, shift = 8.42, angle = 12.4 degrees
Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.68179907 -0.73031354 0.04233404 134.55628275
-0.72995927 -0.67538450 0.10495351 308.10402853
-0.04805721 -0.10245933 -0.99357566 283.32032359
Axis -0.91672636 0.39951261 0.00156579
Axis point 0.00000000 192.14085888 132.24148806
Rotation angle (degrees) 173.50439997
Shift along axis 0.18377410
> volume #6 level 1.828
> select subtract #6
Nothing selected
> hide #!3 models
> volume #6 level 1.172
> show #!3 models
> select add #6
2 models selected
> view matrix models
> #6,0.6818,-0.73031,0.042334,145.51,-0.72996,-0.67538,0.10495,294.75,-0.048057,-0.10246,-0.99358,285.84
> view matrix models
> #6,0.6818,-0.73031,0.042334,133.79,-0.72996,-0.67538,0.10495,309.04,-0.048057,-0.10246,-0.99358,282.76
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.47143,0.87224,0.13024,-67.58,0.87592,-0.44591,-0.18423,88.863,-0.10262,0.20093,-0.97422,246.36
> fitmap #6 inMap #3
Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 3507 points
correlation = 0.7523, correlation about mean = 0.053, overlap = 1436
steps = 84, shift = 11, angle = 9.96 degrees
Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.31271016 0.94213099 0.12083688 -48.05138587
0.94223385 -0.29160641 -0.16480619 65.68302492
-0.12003221 0.16539317 -0.97889599 255.74245569
Axis 0.80789250 0.58932983 0.00025166
Axis point 0.00000000 34.02227920 132.07845223
Rotation angle (degrees) 168.20805262
Shift along axis -0.04702893
> select subtract #6
Nothing selected
> hide #!6 models
> show #!6 models
> select add #6
2 models selected
> view matrix models
> #6,-0.96774,-0.18791,0.16785,278.55,-0.18769,0.98208,0.017294,25.636,-0.16809,-0.014768,-0.98566,287.91
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.96774,-0.18791,0.16785,272.6,-0.18769,0.98208,0.017294,32.876,-0.16809,-0.014768,-0.98566,284.26
> fitmap #6 inMap #3
Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 3507 points
correlation = 0.7248, correlation about mean = 0.05418, overlap = 1264
steps = 60, shift = 9.72, angle = 10.6 degrees
Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.92647017 -0.30027989 0.22690311 266.55888821
-0.26721766 0.94935570 0.16528304 28.41095713
-0.26504293 0.09249729 -0.95978982 282.00607809
Axis -0.14603906 0.98705219 0.06633684
Axis point 153.43261550 0.00000000 122.88099835
Rotation angle (degrees) 165.56984584
Shift along axis 7.82248126
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.92785,-0.005043,0.37292,209.61,0.027742,0.99621,0.082497,-9.3167,-0.37192,0.086891,-0.92419,293.48
> fitmap #6 inMap #3
Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 3507 points
correlation = 0.7519, correlation about mean = 0.05711, overlap = 1436
steps = 100, shift = 5.47, angle = 14.5 degrees
Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.92643320 -0.21423055 0.30955905 249.03084383
-0.21368345 0.97623560 0.03610312 27.35482068
-0.30993696 -0.03270052 -0.95019459 303.95121642
Axis -0.11038513 0.99388850 0.00087774
Axis point 150.47041621 0.00000000 131.94319456
Rotation angle (degrees) 161.84114382
Shift along axis -0.03486954
> select subtract #6
Nothing selected
> hide #!3 models
> hide #!6 models
> show #!3 models
> hide #!3 models
> show #!6 models
> volume flip #6
Opened cryosparc_P4_J219_002_volume_map_sharp.mrc z flip as #7, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #6
> rename CS_P4_J219_sharp_flip id #6
Missing or invalid "models" argument: invalid models specifier
> rename #7 CS_P4_J219_sharp_flip id #6
> save CS_P4_J219_sharp_flip.mrc #6
> show #!3 models
> select add #6
2 models selected
> view matrix models
> #6,0.55385,-0.83087,-0.054,184.1,0.82508,0.55638,-0.098423,-37.993,0.11182,0.009957,0.99368,-50.391
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.55385,-0.83087,-0.054,173.54,0.82508,0.55638,-0.098423,-43.189,0.11182,0.009957,0.99368,-15.893
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.43591,-0.88398,-0.16899,334.46,0.87276,-0.46105,0.1604,51.515,-0.2197,-0.077569,0.97248,45.011
> fitmap #6 inMap #3
Fit map CS_P4_J219_sharp_flip.mrc in map CS_P4_J216_class_2_sharp_flip.mrc
using 3507 points
correlation = 0.9414, correlation about mean = 0.4694, overlap = 2583
steps = 72, shift = 3.53, angle = 4.05 degrees
Position of CS_P4_J219_sharp_flip.mrc (#6) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.45821390 -0.85833568 -0.23086770 342.48607306
0.85407817 -0.49711214 0.15306861 63.33623820
-0.24615139 -0.12704090 0.96086946 56.91191433
Axis -0.16142412 0.00880783 0.98684582
Axis point 157.30567711 132.03749632 0.00000000
Rotation angle (degrees) 119.81679395
Shift along axis 1.43562700
> select subtract #6
Nothing selected
> hide #!3 models
Unsupported scale factor (0.000000) detected on Display1
[Repeated 2 time(s)]
> hide #!6 models
> show #!3 models
> show #!6 models
> hide #!6 models
> color #3 #B1DCFC
> save P4_J216_class_2_sharp.png supersample 3 transparentBackground true
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!3 models
> show #!6 models
> hide #!3 models
> hide #!6 models
> show #!3 models
> color #3 #AFDBFF
> hide #!3 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> color #3 #99BFE5
> hide #!6 models
> view P1
> save P4_J216_class_2_sharp.png supersample 3 transparentBackground true
> hide #!3 models
> show #!6 models
> ui mousemode right translate
> save P4_J219_NU_sharp_flip.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260430_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J243_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J243_003_volume_map_sharp.mrc as #7, grid size 80,80,80,
pixel 3.32, shown at level 1.1, step 1, values float32
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.34351,0.88804,0.30558,-69.154,0.93106,-0.36463,0.013018,61.425,0.12299,0.28005,-0.95208,168.53
> view matrix models
> #7,-0.72211,0.66266,0.19859,108.59,0.68148,0.73076,0.039546,-55.441,-0.11892,0.16389,-0.97928,217.85
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.72211,0.66266,0.19859,107.8,0.68148,0.73076,0.039546,-63.119,-0.11892,0.16389,-0.97928,255.33
> view matrix models
> #7,-0.72211,0.66266,0.19859,116.79,0.68148,0.73076,0.039546,-56.849,-0.11892,0.16389,-0.97928,258.31
> fitmap #7 inMap #6
Fit map cryosparc_P4_J243_003_volume_map_sharp.mrc in map
CS_P4_J219_sharp_flip.mrc using 5116 points
correlation = 0.9377, correlation about mean = 0.7097, overlap = 1.519e+04
steps = 76, shift = 2.16, angle = 10.6 degrees
Position of cryosparc_P4_J243_003_volume_map_sharp.mrc (#7) relative to
CS_P4_J219_sharp_flip.mrc (#6) coordinates:
Matrix rotation and translation
0.96909604 0.16642828 0.18208375 -39.18937125
0.15922720 -0.98578684 0.05358170 236.77616183
0.18841328 -0.02293313 -0.98182203 241.04145354
Axis -0.99224103 -0.08208102 -0.09338329
Axis point 0.00000000 122.34870623 120.06626952
Rotation angle (degrees) 177.79032322
Shift along axis -3.05877231
> select subtract #7
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,-0.62422,0.77517,0.097247,102.65,0.77737,0.62868,-0.021408,-52.876,-0.077732,0.062233,-0.99503,269.09
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.32669,-0.93485,0.13901,287.37,-0.94032,0.30667,-0.14745,222.88,0.095218,-0.17888,-0.97925,277.34
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.32669,-0.93485,0.13901,281.61,-0.94032,0.30667,-0.14745,233.21,0.095218,-0.17888,-0.97925,273.65
> fitmap #7 inMap #6
Fit map cryosparc_P4_J243_003_volume_map_sharp.mrc in map
CS_P4_J219_sharp_flip.mrc using 5116 points
correlation = 0.9419, correlation about mean = 0.7222, overlap = 1.551e+04
steps = 56, shift = 3.52, angle = 7.25 degrees
Position of cryosparc_P4_J243_003_volume_map_sharp.mrc (#7) relative to
CS_P4_J219_sharp_flip.mrc (#6) coordinates:
Matrix rotation and translation
-0.62645631 0.77281267 0.10155321 101.66723571
0.77509514 0.63140454 -0.02357570 -50.90352474
-0.08234076 0.06394425 -0.99455072 266.97848709
Axis 0.42971205 0.90289643 0.01120665
Axis point 70.49413903 0.00000000 130.93970837
Rotation angle (degrees) 174.15511884
Shift along axis 0.71895896
> select subtract #7
Nothing selected
> hide #!6 models
> volume #7 level 1.41
> color #7 #99BFE5
> view P1
> close #7
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J244_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J244_003_volume_map_sharp.mrc as #7, grid size 80,80,80,
pixel 3.32, shown at level 1.05, step 1, values float32
> show #!6 models
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.71966,-0.6805,-0.13788,149.49,-0.69285,-0.71678,-0.078638,342.79,-0.045318,0.15212,-0.98732,223.99
> hide #!6 models
> show #!6 models
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.71966,-0.6805,-0.13788,149.4,-0.69285,-0.71678,-0.078638,338.98,-0.045318,0.15212,-0.98732,258.19
> select subtract #7
Nothing selected
> hide #!6 models
> volume flip #7
Opened cryosparc_P4_J244_003_volume_map_sharp.mrc z flip as #8, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #7
> rename #8 CS_P4_J244_sharp_flip id #7
> save CS_P4_J244_sharp_flip.mrc #7
> color #7 #99BFE5
> volume #7 level 1.156
> save CS_P4_J244_sharp_flip.mrc #7
> save P4_J244_NU_sharp_flip.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_00_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.192, step 1, values float32
> hide #!7 models
> volume #8 level 0.2208
> show #!7 models
> select add #8
2 models selected
> view matrix models #8,1,0,0,1.7912,0,1,0,4.218,0,0,1,1.8536
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.019063,-0.87425,-0.4851,301.31,0.055421,0.48537,-0.87255,194.56,0.99828,-0.010251,0.057705,27.748
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.019063,-0.87425,-0.4851,303.09,0.055421,0.48537,-0.87255,199.03,0.99828,-0.010251,0.057705,19.845
> view matrix models
> #8,0.019063,-0.87425,-0.4851,323.73,0.055421,0.48537,-0.87255,193.31,0.99828,-0.010251,0.057705,17.439
> view matrix models
> #8,0.019063,-0.87425,-0.4851,322.89,0.055421,0.48537,-0.87255,188.18,0.99828,-0.010251,0.057705,19.28
> fitmap #8 inMap #7
Fit map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc in map
CS_P4_J244_sharp_flip.mrc using 14754 points
correlation = 0.481, correlation about mean = 0.07756, overlap = 1756
steps = 112, shift = 13.3, angle = 15.3 degrees
Position of cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) relative to
CS_P4_J244_sharp_flip.mrc (#7) coordinates:
Matrix rotation and translation
0.05423844 -0.87969653 0.47243223 170.87663448
0.10002936 0.47553549 0.87399092 -59.90285646
-0.99350507 -0.00014682 0.11378778 232.31099922
Axis -0.44417982 0.74489379 0.49783284
Axis point 199.16697689 -0.00000000 41.59458970
Rotation angle (degrees) 100.26604714
Shift along axis -4.86917491
> select subtract #8
Nothing selected
> hide #!7 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_01_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.178, step 1, values float32
> hide #!8 models
> volume #9 level 0.1464
> show #!8 models
> select add #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.01099,0.99675,0.079835,4.9565,0.1314,-0.080587,0.98805,-14.68,0.99127,-0.00036851,-0.13186,9.8
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.01099,0.99675,0.079835,10.903,0.1314,-0.080587,0.98805,5.6709,0.99127,-0.00036851,-0.13186,51.786
> view matrix models
> #9,0.01099,0.99675,0.079835,4.7224,0.1314,-0.080587,0.98805,-1.1935,0.99127,-0.00036851,-0.13186,45.788
> fitmap #9 inMap #8
Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 29766 points
correlation = 0.8496, correlation about mean = 0.3082, overlap = 1328
steps = 284, shift = 18.3, angle = 53.9 degrees
Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to
cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99575722 -0.02668322 0.08806571 -8.52134797
-0.09034177 -0.46538978 0.88048323 89.22150736
0.01749075 -0.88470354 -0.46582584 307.69453028
Axis -0.99855360 0.03992375 -0.03601119
Axis point 0.00000000 137.23273941 127.10917488
Rotation angle (degrees) 117.88699495
Shift along axis 0.99063260
> select subtract #9
Nothing selected
> hide #!8 models
> hide #!9 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_02_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
> select add #10
2 models selected
> show #!9 models
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.17462,0.93232,0.31669,19.869,0.21917,0.35036,-0.91061,163.76,-0.95993,-0.089597,-0.26552,316.03
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.17462,0.93232,0.31669,8.7975,0.21917,0.35036,-0.91061,193.69,-0.95993,-0.089597,-0.26552,324.3
> view matrix models
> #10,-0.17462,0.93232,0.31669,5.0809,0.21917,0.35036,-0.91061,186.44,-0.95993,-0.089597,-0.26552,324.52
> fitmap #10 inMap #9
Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20970 points
correlation = 0.8182, correlation about mean = 0.3079, overlap = 1048
steps = 212, shift = 18, angle = 29.3 degrees
Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative
to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates:
Matrix rotation and translation
-0.92160797 -0.37293352 0.10751436 286.70013052
-0.37621404 0.79028143 -0.48365097 141.61699812
0.09540306 -0.48618500 -0.86863249 299.79876520
Axis -0.19795503 0.94611818 -0.25626978
Axis point 158.67244900 0.00000000 168.59386356
Rotation angle (degrees) 179.63327476
Shift along axis 0.40332117
> select subtract #10
Nothing selected
> hide #!9 models
> hide #!10 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_03_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.218, step 1, values float32
> volume #11 level 0.1502
> show #!10 models
> select add #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.73904,-0.47164,0.48101,26.135,-0.11204,0.61802,0.77814,-47.481,-0.66427,-0.62897,0.4039,253.49
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.73904,-0.47164,0.48101,5.5926,-0.11204,0.61802,0.77814,-27.642,-0.66427,-0.62897,0.4039,266.06
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.56676,0.0073102,0.82385,78.335,0.19153,-0.97139,0.14038,216.5,0.80131,0.23736,0.54915,-63.542
> select subtract #11
Nothing selected
> fitmap #11 inMap #10
Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 45754 points
correlation = 0.7333, correlation about mean = -0.04196, overlap = 1268
steps = 132, shift = 23.8, angle = 15.3 degrees
Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative
to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.26691235 0.13508665 -0.95420616 300.80664915
-0.90776913 -0.36770197 0.20186745 274.07355373
-0.32359389 0.92007981 0.22077169 18.93443182
Axis 0.50771970 -0.44579332 -0.73721708
Axis point 236.02557416 49.14154001 0.00000000
Rotation angle (degrees) 134.98497404
Shift along axis 16.58651491
> hide #!10 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_04_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.261, step 1, values float32
> show #!10 models
> hide #!10 models
> select add #12
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,-3.7479,0,1,0,3.9168,0,0,1,20.991
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.79132,-0.13023,0.59737,-27.645,0.22144,0.97176,-0.081485,-12.263,-0.56989,0.19676,0.79781,93.603
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.79132,-0.13023,0.59737,-50.124,0.22144,0.97176,-0.081485,3.5285,-0.56989,0.19676,0.79781,102.68
> view matrix models
> #12,0.79132,-0.13023,0.59737,-48.335,0.22144,0.97176,-0.081485,2.277,-0.56989,0.19676,0.79781,101.98
> view matrix models
> #12,0.79132,-0.13023,0.59737,-41.566,0.22144,0.97176,-0.081485,-1.9637,-0.56989,0.19676,0.79781,101.41
> fitmap #12 inMap #11
Fit map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20956 points
correlation = 0.8514, correlation about mean = 0.04285, overlap = 1430
steps = 80, shift = 7.16, angle = 11.7 degrees
Position of cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) relative
to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates:
Matrix rotation and translation
-0.93263188 0.26201641 0.24808299 197.07280134
-0.29117819 -0.95255879 -0.08858337 308.05329962
0.21310334 -0.15485204 0.96468016 17.95641726
Axis -0.11870856 0.06265985 -0.99095006
Axis point 119.69175871 140.62215054 0.00000000
Rotation angle (degrees) 163.79210928
Shift along axis -21.88556717
> select subtract #12
Nothing selected
> hide #!11 models
> volume #12 level 0.4033
> volume #12 level 0.3453
> color #8 #FCEDFF
> hide #!12 models
> show #!8 models
> hide #!8 models
> show #!9 models
> color #9 #FCEDFF
> hide #!9 models
> show #!10 models
> color #10 #FCEDFF
> hide #!10 models
> show #!11 models
> color #11 #FCEDFF
> hide #!11 models
> show #!12 models
> color #12 #99BFE5
> view P1
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!3 models
> select add #12
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.95369,-0.29732,-0.045496,35.025,0.29889,0.95373,0.032695,-17.906,0.03367,-0.044779,0.99843,26.075
> view matrix models
> #12,-0.8879,0.32078,-0.32974,233.6,0.30063,0.94715,0.1119,-26.299,0.34821,0.00022498,-0.93742,198.42
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.8879,0.32078,-0.32974,232.89,0.30063,0.94715,0.1119,-34.317,0.34821,0.00022498,-0.93742,213.72
> view matrix models
> #12,-0.8879,0.32078,-0.32974,243.25,0.30063,0.94715,0.1119,-55.273,0.34821,0.00022498,-0.93742,214.76
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.88731,0.39919,0.23093,169.34,0.40717,0.91324,-0.014156,-50.796,-0.21654,0.081466,-0.97287,283.71
> fitmap #12 inMap #3
Fit map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 12546 points
correlation = 0.9893, correlation about mean = 0.7632, overlap = 2433
steps = 124, shift = 11, angle = 27.9 degrees
Position of cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) relative
to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.62359754 0.77535022 0.09979057 101.14085164
0.77719680 0.62864768 -0.02769904 -50.42984630
-0.08420957 0.06028386 -0.99462285 268.88184712
Axis 0.43136931 0.90213001 0.00905357
Axis point 70.24601107 0.00000000 131.83510298
Rotation angle (degrees) 174.14674629
Shift along axis 0.56912319
> select subtract #12
Nothing selected
> hide #!12 models
> show #!12 models
> show #!11 models
> select add #11
2 models selected
> view matrix models
> #11,-0.37852,0.89247,0.24538,28.817,0.88041,0.42898,-0.20213,16.101,-0.28566,0.13952,-0.94812,300.03
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.37852,0.89247,0.24538,46.8,0.88041,0.42898,-0.20213,-5.6117,-0.28566,0.13952,-0.94812,300.85
> view matrix models
> #11,-0.37852,0.89247,0.24538,36.63,0.88041,0.42898,-0.20213,-16.953,-0.28566,0.13952,-0.94812,296.6
> fitmap #11 inMap #12
Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 45754 points
correlation = 0.7192, correlation about mean = 0.1299, overlap = 1714
steps = 96, shift = 6.98, angle = 12.7 degrees
Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative
to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates:
Matrix rotation and translation
0.88557701 -0.25567312 -0.38779454 99.27082409
0.32552043 0.93717068 0.12548928 -53.44589150
0.33134544 -0.23736546 0.91316364 -22.95393091
Axis -0.36530839 -0.72400286 0.58512361
Axis point 106.02252826 0.00000000 214.34257569
Rotation angle (degrees) 29.77806268
Shift along axis -11.00037360
> select subtract #11
Nothing selected
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!3 models
> show #!12 models
> hide #!11 models
> show #!10 models
> select add #10
2 models selected
> view matrix models
> #10,-0.49822,0.81176,0.30466,37.524,-0.14214,0.27015,-0.95227,247.33,-0.85532,-0.51775,-0.019207,343.36
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.013344,0.85199,0.52339,-68.961,-0.1627,-0.51831,0.83957,128.11,0.98659,-0.073951,0.14553,-15.381
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.013344,0.85199,0.52339,-45.161,-0.1627,-0.51831,0.83957,119.13,0.98659,-0.073951,0.14553,-13.578
> fitmap #10 inMap #12
Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20970 points
correlation = 0.7101, correlation about mean = 0.02358, overlap = 908.6
steps = 80, shift = 7.98, angle = 9.33 degrees
Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative
to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates:
Matrix rotation and translation
-0.35385865 -0.88893073 0.29083707 267.80089120
-0.02210060 0.31881642 0.94755878 -31.84809054
-0.93503776 0.32887420 -0.13246184 232.75133151
Axis -0.38099533 0.75491227 0.53380711
Axis point 205.22642342 0.00000000 36.94010088
Rotation angle (degrees) 125.71487620
Shift along axis -1.82908632
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.12287,-0.47662,0.87048,95.543,0.19038,-0.87215,-0.45067,269.26,0.97399,0.11035,0.1979,-37.789
> select subtract #10
Nothing selected
> hide #!12 models
> show #!11 models
> show #!12 models
> hide #!10 models
> hide #!12 models
> show #!10 models
> select add #10
2 models selected
> view matrix models
> #10,-0.38685,-0.21971,0.89558,99.669,-0.053858,-0.96416,-0.2598,294.54,0.92057,-0.14874,0.36115,-16.709
> fitmap #10 inMap #11
Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20970 points
correlation = 0.8482, correlation about mean = 0.1221, overlap = 870.1
steps = 88, shift = 3.31, angle = 12.5 degrees
Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative
to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates:
Matrix rotation and translation
-0.32110732 -0.67353914 -0.66575904 357.49560201
0.09667773 -0.72262784 0.68444314 122.97291760
-0.94209527 0.15541563 0.29715733 219.46626263
Axis -0.54292343 0.28359472 0.79044809
Axis point 234.55310205 82.20310947 0.00000000
Rotation angle (degrees) 150.84311237
Shift along axis 14.25842210
> view matrix models
> #10,-0.30509,0.38504,-0.87101,233.77,0.18733,0.92101,0.34153,-54.422,0.93372,-0.058973,-0.35312,61.617
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.30509,0.38504,-0.87101,240.35,0.18733,0.92101,0.34153,-58.712,0.93372,-0.058973,-0.35312,49.559
> view matrix models
> #10,-0.30509,0.38504,-0.87101,238.16,0.18733,0.92101,0.34153,-58.03,0.93372,-0.058973,-0.35312,51.895
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.36524,0.52001,-0.77213,217.65,0.08187,0.84416,0.5298,-55.56,0.9273,0.13029,-0.3509,28.264
> fitmap #10 inMap #11
Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20970 points
correlation = 0.8485, correlation about mean = 0.1929, overlap = 854.7
steps = 140, shift = 18.2, angle = 22.5 degrees
Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative
to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates:
Matrix rotation and translation
-0.33967352 0.22689098 0.91276633 25.87088295
0.00914596 0.97121791 -0.23801704 28.63290177
-0.94049893 -0.07249996 -0.33197214 335.97765353
Axis 0.08835402 0.98928424 -0.11623361
Axis point 129.11230783 0.00000000 160.33867701
Rotation angle (degrees) 110.50039702
Shift along axis -8.44002041
> view matrix models
> #10,-0.23006,0.48061,-0.84622,212.13,0.22993,0.87177,0.43261,-89.291,0.94562,-0.095042,-0.31107,58.162
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.23006,0.48061,-0.84622,206.51,0.22993,0.87177,0.43261,-81.849,0.94562,-0.095042,-0.31107,43.385
> view matrix models
> #10,-0.23006,0.48061,-0.84622,209.88,0.22993,0.87177,0.43261,-83.853,0.94562,-0.095042,-0.31107,44.292
> select subtract #10
Nothing selected
> hide #!10 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!9 models
> show #!10 models
> select add #9
2 models selected
> view matrix models
> #9,0.18919,0.68161,-0.70683,127.56,-0.072128,0.72753,0.68227,-34.663,0.97929,-0.078095,0.1868,-5.196
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.094504,0.99539,-0.016524,13.65,-0.46578,0.02954,-0.88441,305.71,-0.87984,0.091276,0.46642,193.56
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.094504,0.99539,-0.016524,15.801,-0.46578,0.02954,-0.88441,306.87,-0.87984,0.091276,0.46642,176.78
> view matrix models
> #9,0.094504,0.99539,-0.016524,12.042,-0.46578,0.02954,-0.88441,307.73,-0.87984,0.091276,0.46642,167.03
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.21351,-0.97318,0.085687,220.62,-0.11603,0.061829,0.99132,14.069,-0.97003,-0.2216,-0.099713,290.21
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.21351,-0.97318,0.085687,223.99,-0.11603,0.061829,0.99132,9.6501,-0.97003,-0.2216,-0.099713,279.71
> fitmap #9 inMap #10
Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 29766 points
correlation = 0.8261, correlation about mean = 0.3518, overlap = 1268
steps = 228, shift = 10.5, angle = 43.8 degrees
Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.79231406 -0.50183310 0.34698987 259.09489231
0.60835065 -0.60661249 0.51179172 70.83831660
-0.04634564 0.61659129 0.78591810 -47.09681091
Axis 0.08862868 0.33264264 0.93887903
Axis point 119.55771099 88.88471782 0.00000000
Rotation angle (degrees) 143.75577737
Shift along axis 2.30887434
> select subtract #9
Nothing selected
> hide #!9 models
> hide #!10 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!9 models
> show #!9 models
> select add #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.57009,0.77789,0.26434,-76.801,0.087184,0.26265,-0.96094,232.01,-0.81694,0.57087,0.081917,150.81
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.57009,0.77789,0.26434,-65.422,0.087184,0.26265,-0.96094,221.32,-0.81694,0.57087,0.081917,140.75
> view matrix models
> #8,0.57009,0.77789,0.26434,-76.259,0.087184,0.26265,-0.96094,220.33,-0.81694,0.57087,0.081917,139.28
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.35163,-0.43011,0.83148,20.753,0.096433,0.90012,0.42483,-70.009,-0.93116,-0.069204,0.35799,194.15
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.35163,-0.43011,0.83148,32.249,0.096433,0.90012,0.42483,-69.075,-0.93116,-0.069204,0.35799,199.19
> fitmap #8 inMap #9
Fit map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 14754 points
correlation = 0.886, correlation about mean = 0.3322, overlap = 930.7
steps = 164, shift = 11.7, angle = 31.5 degrees
Position of cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) relative to
cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.99392076 -0.10814474 0.02064566 12.78899705
-0.02517844 -0.40582068 -0.91360584 308.93876287
0.10718010 0.90753198 -0.40607651 52.31471926
Axis 0.99784036 -0.04741407 0.04545901
Axis point 0.00000000 137.80284162 126.13315110
Rotation angle (degrees) 114.14129203
Shift along axis 0.49150880
> select subtract #8
Nothing selected
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> view P1
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!8 models
> show #!12 models
> view P1
> select add #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.17056,0.37082,0.91291,-61.936,0.033776,0.92374,-0.38153,50.195,-0.98477,0.095906,0.14502,217.51
> select subtract #8
Nothing selected
> hide #!12 models
> show #!9 models
> select add #9
2 models selected
> view matrix models
> #9,0.22431,-0.86548,-0.44791,277.63,0.10958,-0.43431,0.89407,50.356,-0.96834,-0.24963,-0.0025846,282.76
> fitmap #9 inMap #8
Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 29766 points
correlation = 0.8496, correlation about mean = 0.3079, overlap = 1328
steps = 196, shift = 4.92, angle = 23.1 degrees
Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to
cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99577299 -0.02696715 0.08780046 -8.42294333
-0.09023986 -0.46536786 0.88050527 89.20116331
0.01711480 -0.88470646 -0.46583426 307.74421532
Axis -0.99855897 0.03998603 -0.03579261
Axis point 0.00000000 137.24012810 127.13677639
Rotation angle (degrees) 117.88604570
Shift along axis 0.96263749
> select subtract #9
Nothing selected
> select add #9
2 models selected
> select subtract #9
Nothing selected
> hide #!8 models
> hide #!9 models
> show #!9 models
> show #!10 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!9 models
> select add #10
2 models selected
> view matrix models
> #10,-0.15057,0.45945,-0.87535,204.11,-0.21614,0.84872,0.48265,-19.059,0.96468,0.26187,-0.028487,-39.785
> fitmap #10 inMap #8
Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 20970 points
correlation = 0.8656, correlation about mean = 0.3963, overlap = 1232
steps = 148, shift = 6.34, angle = 30.8 degrees
Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative
to cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates:
Matrix rotation and translation
-0.99459983 0.06769619 -0.07866640 263.08124995
0.09074118 0.93510189 -0.34256458 42.75279763
0.05037079 -0.34785296 -0.93619501 298.73878944
Axis -0.04031220 -0.98362390 0.17566718
Axis point 125.67832095 0.00000000 157.57753081
Rotation angle (degrees) 176.23911220
Shift along axis -0.17945663
> show #!8 models
> hide #!9 models
> select subtract #10
Nothing selected
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!11 models
> hide #!10 models
> show #!10 models
> select add #11
2 models selected
> view matrix models
> #11,0.83789,-0.53148,-0.12435,93.216,-0.53452,-0.84509,0.010318,306.1,-0.11057,0.05782,-0.99219,291.46
> view matrix models
> #11,0.87567,0.38049,0.29737,-84.014,0.47018,-0.53126,-0.70477,229.85,-0.11018,0.75696,-0.64411,156.03
> view matrix models
> #11,0.99273,0.070823,-0.097356,-6.1982,0.016369,-0.88055,-0.47367,302.86,-0.11927,0.46863,-0.87531,225.51
> fitmap #11 inMap #10
Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 45754 points
correlation = 0.7386, correlation about mean = -0.02581, overlap = 1355
steps = 168, shift = 17.3, angle = 31.8 degrees
Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative
to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.38917965 0.05095816 -0.91975131 323.90582539
-0.15837916 -0.98730156 0.01231516 285.52055130
-0.90744434 0.15046225 0.39230839 175.68159882
Axis 0.55013716 -0.04900950 -0.83363492
Axis point 230.74773970 125.72052254 0.00000000
Rotation angle (degrees) 172.78707980
Shift along axis 17.74509610
> select subtract #11
Nothing selected
> hide #!11 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> view P1
> show #!12 models
> ui mousemode right translate
> save P4_J242_class_4_sharp.png supersample 3 transparentBackground true
> hide #!12 models
> show #!11 models
> save P4_J242_class_3_sharp.png supersample 3 transparentBackground true
> hide #!11 models
> show #!10 models
> save P4_J242_class_2_sharp.png supersample 3 transparentBackground true
> hide #!10 models
> show #!9 models
> view P1
[Repeated 1 time(s)]
> save P4_J242_class_1_sharp.png supersample 3 transparentBackground true
> hide #!9 models
> show #!8 models
> save P4_J242_class_0_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
Unsupported scale factor (0.000000) detected on Display1
[Repeated 2 time(s)]
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J117_class_00_00162_volume_sharp.mrc"
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
> hide #!8 models
> select add #13
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #13,1,0,0,6.2015,0,1,0,0.69431,0,0,1,-17.516
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.13264,-0.68512,-0.71625,337.99,0.0019176,-0.72281,0.69104,120.39,-0.99116,0.090284,0.097186,224.71
> view matrix models
> #13,0.0040424,0.12352,-0.99233,257.27,0.14964,-0.98124,-0.12153,245.92,-0.98873,-0.148,-0.02245,270.75
> select subtract #13
Nothing selected
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!10 models
> fitmap #13 inMap #10
Fit map cryosparc_P4_J117_class_00_00162_volume_sharp.mrc in map
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 20961 points
correlation = 0.8109, correlation about mean = 0.2077, overlap = 1054
steps = 92, shift = 12.7, angle = 18.1 degrees
Position of cryosparc_P4_J117_class_00_00162_volume_sharp.mrc (#13) relative
to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.98193657 -0.07856914 0.17212633 243.32837219
0.00195692 -0.91387700 -0.40598645 309.66348462
0.18920029 -0.39831610 0.89752300 41.87114917
Axis 0.09277951 -0.20652448 0.97403265
Axis point 116.38449758 161.85402651 0.00000000
Rotation angle (degrees) 177.63092236
Shift along axis -0.59333628
> hide #!10 models
> hide #!13 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J117_class_01_00162_volume_sharp.mrc"
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
> select add #14
2 models selected
> view matrix models
> #14,-0.39254,-0.77748,0.49135,234.79,-0.04345,-0.51796,-0.8543,320.26,0.91871,-0.3567,0.16954,27.288
> view matrix models
> #14,-0.061348,0.89979,0.432,-25.376,-0.288,-0.43036,0.85548,115.2,0.95566,-0.071931,0.28554,-30.976
> view matrix models
> #14,-0.046716,0.65995,-0.74985,161.94,-0.070464,0.74662,0.6615,-44.914,0.99642,0.08374,0.011624,-20.712
> select subtract #14
Nothing selected
> show #!13 models
> fitmap #14 inMap #13
Fit map cryosparc_P4_J117_class_01_00162_volume_sharp.mrc in map
cryosparc_P4_J117_class_00_00162_volume_sharp.mrc using 20968 points
correlation = 0.846, correlation about mean = 0.3465, overlap = 1110
steps = 132, shift = 18.5, angle = 19.5 degrees
Position of cryosparc_P4_J117_class_01_00162_volume_sharp.mrc (#14) relative
to cryosparc_P4_J117_class_00_00162_volume_sharp.mrc (#13) coordinates:
Matrix rotation and translation
-0.99955515 0.02982234 0.00035424 260.68209471
-0.00628473 -0.19900464 -0.97997839 284.54003350
-0.02915475 -0.97954468 0.19910354 244.04930876
Axis 0.00930049 0.63278447 -0.77427212
Axis point 133.98017190 240.03303746 0.00000000
Rotation angle (degrees) 178.66392593
Shift along axis -6.48359029
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J117_class_02_00162_volume_sharp.mrc"
Opened cryosparc_P4_J117_class_02_00162_volume_sharp.mrc as #15, grid size
128,128,128, pixel 2.08, shown at level 0.251, step 1, values float32
> hide #!13 models
> select add #14
2 models selected
> show #!12 models
> select subtract #14
Nothing selected
> hide #!14 models
> select add #15
2 models selected
> view matrix models
> #15,-0.98221,0.18526,0.030552,219.51,0.18651,0.98144,0.044675,-26.394,-0.021708,0.049578,-0.99853,243.73
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.98221,0.18526,0.030552,234.62,0.18651,0.98144,0.044675,-36.86,-0.021708,0.049578,-0.99853,271.78
> fitmap #15 inMap #12
Fit map cryosparc_P4_J117_class_02_00162_volume_sharp.mrc in map
cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20967 points
correlation = 0.781, correlation about mean = 0.07908, overlap = 1573
steps = 76, shift = 10.9, angle = 6.65 degrees
Position of cryosparc_P4_J117_class_02_00162_volume_sharp.mrc (#15) relative
to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates:
Matrix rotation and translation
0.82536305 0.56130744 0.06090799 -57.36751075
-0.56057744 0.82755504 -0.03009290 101.38226037
-0.06729608 -0.00930608 0.99768964 1.14989876
Axis 0.01840555 0.11351744 -0.99336550
Axis point 134.55599767 144.37243816 0.00000000
Rotation angle (degrees) 34.38068857
Shift along axis 9.31050435
> volume flip #15
Opened cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip as #16, grid
size 128,128,128, pixel 2.08, shown at step 1, values float32
> close #15
> select add #16
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.81511,-0.57721,0.04929,312.41,0.52972,-0.77708,-0.33992,218.14,0.2345,-0.25096,0.93916,8.6526
> fitmap #15 inMap #12
No atoms or maps for #15
> fitmap #16 inMap #12
Fit map cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip in map
cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20967 points
correlation = 0.9777, correlation about mean = 0.7437, overlap = 2747
steps = 108, shift = 14.1, angle = 17.5 degrees
Position of cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip (#16)
relative to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12)
coordinates:
Matrix rotation and translation
0.94024990 -0.32652551 -0.09649458 65.60674301
-0.33221344 -0.94188358 -0.04989541 307.74881291
-0.07459454 0.07897095 -0.99408211 253.25354142
Axis 0.98493295 -0.16738329 -0.04347315
Axis point 0.00000000 155.23786381 133.19610246
Rotation angle (degrees) 176.24909728
Shift along axis 2.09650544
> select subtract #16
Nothing selected
> rename #16 CS_P4_J117_class_02_sharp_flip.mrc id #15
> save CS_P4_J117_class_02_sharp_flip.mrc #15
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J117_class_03_00162_volume_sharp.mrc"
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
> hide #!12 models
> hide #!15 models
> select add #16
2 models selected
> show #!14 models
> view matrix models
> #16,0.00021536,0.34795,0.93751,-37.63,0.50671,0.80821,-0.30007,0.053261,-0.86212,0.47511,-0.17613,183.13
> hide #!14 models
> view matrix models
> #16,0.63015,0.10301,-0.76961,125.95,-0.74582,0.35606,-0.56301,261.02,0.21603,0.92877,0.3012,-81.743
> view matrix models
> #16,0.63277,-0.43368,-0.64151,190.37,0.75188,0.14602,0.64293,-47.242,-0.18515,-0.88916,0.41847,227.83
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!11 models
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.63277,-0.43368,-0.64151,206.09,0.75188,0.14602,0.64293,-70.694,-0.18515,-0.88916,0.41847,249.05
> view matrix models
> #16,0.63277,-0.43368,-0.64151,204.5,0.75188,0.14602,0.64293,-75.196,-0.18515,-0.88916,0.41847,240.94
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.30976,-0.38252,-0.87047,346.06,0.94397,-0.2334,-0.23335,63.654,-0.1139,-0.89398,0.43339,230.67
> fitmap #16 inMap #11
Fit map cryosparc_P4_J117_class_03_00162_volume_sharp.mrc in map
cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20958 points
correlation = 0.9023, correlation about mean = 0.3197, overlap = 1117
steps = 184, shift = 6.54, angle = 53.8 degrees
Position of cryosparc_P4_J117_class_03_00162_volume_sharp.mrc (#16) relative
to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates:
Matrix rotation and translation
0.41743274 -0.19488532 -0.88756388 222.32976103
-0.90862481 -0.10271919 -0.40478358 322.57606660
-0.01228347 0.97543246 -0.21995599 21.59894000
Axis 0.77392148 -0.49079151 -0.40021149
Axis point 0.00000000 222.40854643 197.20887777
Rotation angle (degrees) 116.91198346
Shift along axis 5.10403978
> select subtract #16
Nothing selected
> hide #!11 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J117_class_04_00162_volume_sharp.mrc"
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
> hide #!16 models
> select add #17
2 models selected
> show #!13 models
> hide #!13 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!17 models
> show #!17 models
> view matrix models
> #17,-0.0034658,-0.079884,-0.9968,294.42,-0.15421,0.98492,-0.078396,35.543,0.98803,0.15344,-0.015732,-30.795
> fitmap #17 inMap #10
Fit map cryosparc_P4_J117_class_04_00162_volume_sharp.mrc in map
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 20958 points
correlation = 0.8416, correlation about mean = 0.3036, overlap = 1170
steps = 148, shift = 13.9, angle = 32.2 degrees
Position of cryosparc_P4_J117_class_04_00162_volume_sharp.mrc (#17) relative
to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.73519379 0.67627298 0.04631360 -60.93633283
-0.67522557 0.73664284 -0.03778583 134.15115598
-0.05967011 -0.00349222 0.99821205 3.94076312
Axis 0.02528875 0.07815439 -0.99662047
Axis point 141.29888305 145.62167557 0.00000000
Rotation angle (degrees) 42.69072745
Shift along axis 5.01605257
> select subtract #17
Nothing selected
> hide #!10 models
> show #!10 models
> hide #!17 models
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> show #!13 models
> hide #!10 models
> color #13 #FCEDFF
> hide #!13 models
> show #!14 models
> color #14 #FCEDFF
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!16 models
> color #16 #FCEDFF
> hide #!16 models
> show #!17 models
> color #17 #FCEDFF
> show #!15 models
> hide #!17 models
> color #15 #99BFE5
> volume #15 level 0.3349
> ui mousemode right translate
> view P1
[Repeated 1 time(s)]
> save P4_J117_class_2_sharp.png supersample 3 transparentBackground true
> hide #!15 models
> show #!13 models
> save P4_J117_class_0_sharp.png supersample 3 transparentBackground true
> hide #!13 models
> show #!14 models
> save P4_J117_class_1_sharp.png supersample 3 transparentBackground true
> hide #!14 models
> show #!16 models
> save P4_J117_class_3_sharp.png supersample 3 transparentBackground true
> hide #!16 models
> show #!17 models
> save P4_J117_class_4_sharp.png supersample 3 transparentBackground true
[Repeated 1 time(s)]
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J120_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J120_002_volume_map_sharp.mrc as #18, grid size 80,80,80,
pixel 3.32, shown at level 1.08, step 1, values float32
> hide #!17 models
> show #!15 models
> select add #18
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.9199,0.35329,0.17023,-57.439,0.37414,-0.92071,-0.11099,219.04,0.11752,0.16579,-0.97913,208.75
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.9199,0.35329,0.17023,-56.147,0.37414,-0.92071,-0.11099,218.08,0.11752,0.16579,-0.97913,234.23
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.47537,0.87487,0.092902,-59.652,0.86989,-0.48319,0.099115,73.008,0.1316,0.033698,-0.99073,251.23
> volume flip #18
Opened cryosparc_P4_J120_002_volume_map_sharp.mrc z flip as #19, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> select subtract #18
Nothing selected
> close #18
> select add #19
2 models selected
> view matrix models
> #19,0.011836,0.9987,-0.049536,1.5471,-0.96239,0.024824,0.27053,210.58,0.27141,0.044471,0.96144,-38.44
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.011836,0.9987,-0.049536,5.1894,-0.96239,0.024824,0.27053,209.75,0.27141,0.044471,0.96144,-23.291
> fitmap #19 inMap #15
Fit map cryosparc_P4_J120_002_volume_map_sharp.mrc z flip in map
CS_P4_J117_class_02_sharp_flip.mrc using 5118 points
correlation = 0.9182, correlation about mean = 0.533, overlap = 3573
steps = 76, shift = 9.96, angle = 10.7 degrees
Position of cryosparc_P4_J120_002_volume_map_sharp.mrc z flip (#19) relative
to CS_P4_J117_class_02_sharp_flip.mrc (#15) coordinates:
Matrix rotation and translation
-0.48058823 -0.86458262 0.14673736 288.72558748
0.85464108 -0.49926017 -0.14257599 104.76974006
0.19652884 0.05688743 0.97884638 -28.97188121
Axis 0.11519876 -0.02875674 0.99292613
Axis point 115.59153027 135.80137987 0.00000000
Rotation angle (degrees) 120.03315219
Shift along axis 1.48105620
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.89305,-0.32489,-0.3113,106.99,0.34183,0.93976,-0.00013805,-25.175,0.29259,-0.10629,0.95031,-3.3753
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.89305,-0.32489,-0.3113,96.178,0.34183,0.93976,-0.00013805,-42.263,0.29259,-0.10629,0.95031,-5.1551
> fitmap #19 inMap #15
Fit map cryosparc_P4_J120_002_volume_map_sharp.mrc z flip in map
CS_P4_J117_class_02_sharp_flip.mrc using 5118 points
correlation = 0.9187, correlation about mean = 0.5356, overlap = 3578
steps = 76, shift = 8.31, angle = 8.52 degrees
Position of cryosparc_P4_J120_002_volume_map_sharp.mrc z flip (#19) relative
to CS_P4_J117_class_02_sharp_flip.mrc (#15) coordinates:
Matrix rotation and translation
-0.47913034 0.85546358 0.19651003 54.96243137
-0.86530880 -0.49790427 0.05772364 303.37608678
0.14722365 -0.14238471 0.97880120 3.73022055
Axis -0.11546470 0.02843878 -0.99290440
Axis point 115.58296139 135.79077530 0.00000000
Rotation angle (degrees) 119.94157891
Shift along axis -1.42232844
> hide #!19 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!19 models
> select subtract #19
Nothing selected
> show #!15 models
> hide #!15 models
> rename #19 CS_P4_J120_sharp_flip id #18
> save CS_P4_J120_sharp_flip.mrc #18
> volume #18 level 1.185
> volume #18 level 1.639
> volume #18 step 2
> volume #18 step 1
> show #!15 models
> volume #18 level 1.559
> hide #!15 models
> volume #18 level 1.292
> view P1
> color #18 #99BFE5
> show #!17 models
> hide #!17 models
> hide #!18 models
> show #!18 models
> save P4_J120_NU_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_00_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.175, step 1, values float32
> select add #19
2 models selected
> hide #!18 models
> show #!18 models
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #19,1,0,0,-7.1681,0,1,0,-1.6755,0,0,1,29.407
> fitmap #19 inMap #18
Fit map cryosparc_P4_J169_class_00_00182_volume_sharp.mrc in map
CS_P4_J120_sharp_flip.mrc using 20970 points
correlation = 0.3797, correlation about mean = 0.05313, overlap = 2374
steps = 192, shift = 6.4, angle = 17.5 degrees
Position of cryosparc_P4_J169_class_00_00182_volume_sharp.mrc (#19) relative
to CS_P4_J120_sharp_flip.mrc (#18) coordinates:
Matrix rotation and translation
0.64594502 0.66965380 0.36649532 -93.21942227
-0.65111130 0.73392063 -0.19342850 149.32350272
-0.39850860 -0.11368507 0.91009153 102.27587247
Axis 0.05217441 0.50052557 -0.86414813
Axis point 153.99219258 219.18137479 0.00000000
Rotation angle (degrees) 49.83592965
Shift along axis -18.50494005
> select subtract #19
Nothing selected
> hide #!18 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_01_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.189, step 1, values float32
> hide #!19 models
> show #!17 models
> select add #20
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.023382,0.1088,0.99379,-27.517,0.050205,0.99268,-0.10986,9.6432,-0.99847,0.052462,0.017749,251.64
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!14 models
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.023382,0.1088,0.99379,-22.964,0.050205,0.99268,-0.10986,7.1023,-0.99847,0.052462,0.017749,242.74
> ui mousemode right "rotate selected models"
> view matrix models
> #20,-0.029978,-0.71994,-0.69339,335.92,-0.21064,-0.67357,0.70847,177,-0.9771,0.16729,-0.13145,243.19
> ui mousemode right "translate selected models"
> view matrix models
> #20,-0.029978,-0.71994,-0.69339,328.25,-0.21064,-0.67357,0.70847,170.9,-0.9771,0.16729,-0.13145,240.41
> fitmap #20 inMap #14
Fit map cryosparc_P4_J169_class_01_00182_volume_sharp.mrc in map
cryosparc_P4_J117_class_01_00162_volume_sharp.mrc using 20954 points
correlation = 0.8829, correlation about mean = 0.4124, overlap = 1200
steps = 104, shift = 14, angle = 14 degrees
Position of cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) relative
to cryosparc_P4_J117_class_01_00162_volume_sharp.mrc (#14) coordinates:
Matrix rotation and translation
-0.94773816 0.28655181 -0.14028702 243.79600144
-0.24891252 -0.93914826 -0.23673424 326.23627964
-0.19958693 -0.18944287 0.96139298 60.20896934
Axis 0.08744550 0.10965027 -0.99011621
Axis point 147.27291182 149.47535150 0.00000000
Rotation angle (degrees) 164.31164420
Shift along axis -2.52311906
> select subtract #20
Nothing selected
> hide #!14 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_02_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.216, step 1, values float32
> hide #!20 models
> select add #21
2 models selected
> view matrix models #21,1,0,0,-13.073,0,1,0,8.3491,0,0,1,8.6967
> ui mousemode right "rotate selected models"
> view matrix models
> #21,-0.06365,0.67952,0.73089,-53.58,-0.2928,0.68743,-0.66461,177.89,-0.95405,-0.25631,0.15521,285.48
> view matrix models
> #21,0.10048,-0.44353,0.89061,41.096,0.13793,-0.88029,-0.45395,284.46,0.98533,0.16846,-0.027275,-4.3073
> fitmap #21 inMap #20
Fit map cryosparc_P4_J169_class_02_00182_volume_sharp.mrc in map
cryosparc_P4_J169_class_01_00182_volume_sharp.mrc using 20962 points
correlation = 0.7829, correlation about mean = 0.1539, overlap = 900.6
steps = 188, shift = 21.5, angle = 32 degrees
Position of cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) relative
to cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) coordinates:
Matrix rotation and translation
-0.75680258 0.56772680 0.32393846 109.96194933
0.37589927 0.78345603 -0.49487007 56.85693302
-0.53474254 -0.25275071 -0.80632963 338.09031391
Axis 0.26532092 0.94096581 -0.21020979
Axis point 90.65236627 0.00000000 161.68382083
Rotation angle (degrees) 152.85290905
Shift along axis 11.60574300
> show #!20 models
> select subtract #21
Nothing selected
> select add #21
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.31625,-0.43913,0.84092,24.723,-0.35094,-0.87769,-0.32634,336.73,0.88138,-0.19191,-0.43168,94.219
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.23561,0.79493,-0.55908,75.399,0.21977,0.51679,0.82742,-71.321,0.94667,-0.31782,-0.052938,48.925
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.23561,0.79493,-0.55908,69.861,0.21977,0.51679,0.82742,-70.077,0.94667,-0.31782,-0.052938,40.098
> fitmap #21 inMap #20
Fit map cryosparc_P4_J169_class_02_00182_volume_sharp.mrc in map
cryosparc_P4_J169_class_01_00182_volume_sharp.mrc using 20962 points
correlation = 0.8883, correlation about mean = 0.4082, overlap = 1398
steps = 80, shift = 8.95, angle = 4.79 degrees
Position of cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) relative
to cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) coordinates:
Matrix rotation and translation
-0.99875153 -0.02706229 -0.04198798 281.31180443
0.03395891 -0.98426911 -0.17338138 286.61926959
-0.03663538 -0.17459079 0.98395929 28.58358251
Axis -0.01973976 -0.08736459 0.99598081
Axis point 138.73615561 146.72655614 0.00000000
Rotation angle (degrees) 178.24454217
Shift along axis -2.12470384
> select subtract #21
Nothing selected
> hide #!20 models
> hide #!21 models
> show #!21 models
> show #!20 models
> hide #!21 models
> show #!21 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_03_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc as #22, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
> hide #!20 models
> hide #!21 models
> select add #22
2 models selected
> show #!18 models
> ui mousemode right "rotate selected models"
> view matrix models
> #22,0.80286,-0.54835,0.23395,74.113,-0.54307,-0.83458,-0.092472,336.96,0.24595,-0.052807,-0.96784,209.56
> view matrix models
> #22,0.23802,0.97115,0.01476,-30.605,0.97056,-0.2384,0.03436,32.801,0.036887,0.0061467,-0.9993,233.87
> ui mousemode right "translate selected models"
> view matrix models
> #22,0.23802,0.97115,0.01476,-35.135,0.97056,-0.2384,0.03436,31.843,0.036887,0.0061467,-0.9993,265.72
> view matrix models
> #22,0.23802,0.97115,0.01476,-30.091,0.97056,-0.2384,0.03436,32.303,0.036887,0.0061467,-0.9993,265.71
> select subtract #22
Nothing selected
> hide #!18 models
> volume flip #22
Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip as #23, grid
size 128,128,128, pixel 2.08, shown at step 1, values float32
> close #22
> show #!21 models
> hide #!21 models
> show #!18 models
> select add #23
2 models selected
> view matrix models
> #23,0.23802,0.97115,0.01476,-34.192,0.97056,-0.2384,0.03436,27.412,0.036887,0.0061467,-0.9993,278.73
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.23315,-0.92003,-0.31494,337.04,0.93397,-0.30205,0.19095,18.61,-0.27081,-0.24962,0.92971,78.293
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.23315,-0.92003,-0.31494,335.86,0.93397,-0.30205,0.19095,18.866,-0.27081,-0.24962,0.92971,88.616
> fitmap #23 inMap #18
Fit map cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip in map
CS_P4_J120_sharp_flip.mrc using 20952 points
correlation = 0.9077, correlation about mean = 0.6695, overlap = 1.202e+04
steps = 60, shift = 4.34, angle = 10.2 degrees
Position of cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip (#23)
relative to CS_P4_J120_sharp_flip.mrc (#18) coordinates:
Matrix rotation and translation
0.17479617 -0.97573598 0.13185442 219.49728105
0.98179238 0.18284123 0.05150543 -32.00811477
-0.07436413 0.12045072 0.98993010 -9.54926019
Axis 0.03500529 0.10470244 0.99388733
Axis point 128.78581299 116.22335978 0.00000000
Rotation angle (degrees) 79.99211268
Shift along axis -5.15865059
> select subtract #23
Nothing selected
> hide #!18 models
> rename #23 CS_P4_J169_class_03_sharp_flip id #22
> save CS_P4_J169_class_03_sharp_flip.mrc #22
> show #!21 models
> hide #!21 models
> show #!18 models
> hide #!18 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_04_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.171, step 1, values float32
> hide #!22 models
> show #!21 models
> select add #23
2 models selected
> view matrix models #23,1,0,0,62.54,0,1,0,-0.93224,0,0,1,-9.0713
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.11131,-0.99321,-0.033862,304.62,-0.95598,-0.11633,0.2694,223.09,-0.27151,0.0023841,-0.96243,297.1
> view matrix models
> #23,0.14785,0.8725,0.4657,-3.2346,-0.24604,0.48852,-0.83714,210.48,-0.95792,0.0091875,0.2869,210.23
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.14785,0.8725,0.4657,-72.613,-0.24604,0.48852,-0.83714,211.81,-0.95792,0.0091875,0.2869,205.44
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.12372,0.72067,0.68215,-49.094,0.065146,0.69184,-0.7191,130.45,-0.99018,-0.044529,-0.13254,274.4
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.12372,0.72067,0.68215,-52.059,0.065146,0.69184,-0.7191,130.58,-0.99018,-0.044529,-0.13254,270.2
> fitmap #23 inMap #21
Fit map cryosparc_P4_J169_class_04_00182_volume_sharp.mrc in map
cryosparc_P4_J169_class_02_00182_volume_sharp.mrc using 20956 points
correlation = 0.8996, correlation about mean = 0.4033, overlap = 1373
steps = 168, shift = 14.7, angle = 39.5 degrees
Position of cryosparc_P4_J169_class_04_00182_volume_sharp.mrc (#23) relative
to cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) coordinates:
Matrix rotation and translation
-0.99961182 0.01552465 -0.02313457 267.26750037
0.02397017 0.90245504 -0.43011668 70.06567251
0.01420050 -0.43050425 -0.90247684 305.57661651
Axis -0.01012464 -0.97530665 0.22062281
Axis point 131.76679627 0.00000000 162.02424501
Rotation angle (degrees) 178.90328205
Shift along axis -3.62433410
> select subtract #23
Nothing selected
> hide #!23 models
> hide #!21 models
> show #!23 models
> volume #23 level 0.1996
> hide #!23 models
> show #!22 models
> volume #22 level 0.2715
> hide #!22 models
> show #!21 models
> volume #21 level 0.2481
> hide #!21 models
> show #!20 models
> volume #20 level 0.198
> hide #!20 models
> show #!19 models
> volume #19 level 0.1357
> volume #19 level 0.1565
> color #9 #FCEDFF
> show #!9 models
> hide #!9 models
> color #19 #FCEDFF
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> hide #!19 models
> show #!20 models
> color #20 #FCEDFF
> hide #!20 models
> show #!21 models
> show #!20 models
> hide #!20 models
> color #21 #FCEDFF
> hide #!21 models
> show #!22 models
> show #!23 models
> hide #!22 models
> color #23 #FCEDFF
> color #22 #99BFE5
> show #!22 models
> hide #!23 models
> hide #!22 models
> show #!22 models
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> view P1
> save P4_J169_class_3_sharp.png supersample 3 transparentBackground true
> hide #!22 models
> show #!19 models
> save P4_J169_class_0_sharp.png supersample 3 transparentBackground true
> hide #!19 models
> show #!20 models
> save P4_J169_class_1_sharp.png supersample 3 transparentBackground true
> hide #!20 models
> show #!21 models
> save P4_J169_class_2_sharp.png supersample 3 transparentBackground true
> hide #!21 models
> show #!22 models
> show #!23 models
> hide #!22 models
> save P4_J169_class_4_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J176_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J176_002_volume_map_sharp.mrc as #24, grid size 80,80,80,
pixel 3.32, shown at level 1.05, step 1, values float32
> show #!22 models
> hide #!23 models
> select add #24
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.60544,-0.7944,-0.048687,168.77,-0.79404,-0.60707,0.031193,325.29,-0.054337,0.019774,-0.99833,244.32
> view matrix models
> #24,0.59955,-0.80023,-0.012763,166.07,-0.79939,-0.59954,0.03913,324.05,-0.038965,-0.013258,-0.99915,246.8
> view matrix models
> #24,0.55506,-0.74882,-0.36218,207.08,-0.8209,-0.56341,-0.093219,337.96,-0.13425,0.34906,-0.92744,201.93
> view matrix models
> #24,0.18767,0.98161,-0.034938,-17.516,0.95411,-0.19063,-0.23093,58.314,-0.23335,0.010004,-0.97234,267.28
> volume flip #24
Opened cryosparc_P4_J176_002_volume_map_sharp.mrc z flip as #25, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #24
> select add #25
2 models selected
> view matrix models
> #25,-0.63444,0.77032,-0.064025,129.07,-0.77136,-0.63629,-0.011971,326.31,-0.04996,0.041792,0.99788,-43.633
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.63444,0.77032,-0.064025,133.77,-0.77136,-0.63629,-0.011971,326.45,-0.04996,0.041792,0.99788,5.2846
> fitmap #25 inMap #22
Fit map cryosparc_P4_J176_002_volume_map_sharp.mrc z flip in map
CS_P4_J169_class_03_sharp_flip.mrc using 5115 points
correlation = 0.927, correlation about mean = 0.5943, overlap = 3935
steps = 92, shift = 11.4, angle = 9.34 degrees
Position of cryosparc_P4_J176_002_volume_map_sharp.mrc z flip (#25) relative
to CS_P4_J169_class_03_sharp_flip.mrc (#22) coordinates:
Matrix rotation and translation
-0.48979714 -0.86290735 -0.12445753 333.02911722
0.86312907 -0.50006428 0.07031310 74.16708713
-0.12291046 -0.07298376 0.98973047 29.10111268
Axis -0.08273609 -0.00089324 0.99657109
Axis point 146.24021491 133.58927656 0.00000000
Rotation angle (degrees) 120.00433179
Shift along axis 1.38155071
> select subtract #25
Nothing selected
> rename #25 CS_P4_J176_NU_sharp_flip id #24
> save CS_P4_J176_NU_sharp_flip.mrc #24
> hide #!22 models
> volume #24 level 1.757
> volume #24 level 1.364
> color #24 #99BFE5
> volume #24 level 1.6
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> view P1
> save CS_P4_J176_NU_sharp.png supersample 3 transparentBackground true
> open "/Users/peiyuyu/Documents/Goethe University/19. Model Building/2. AcrF
> Project/1. Apo-form/LG-F_Apo/Map/cryosparc_P10_J41_007_volume_map_sharp.mrc"
Opened cryosparc_P10_J41_007_volume_map_sharp.mrc as #25, grid size
320,320,320, pixel 0.831, shown at level 0.123, step 2, values float32
> hide #!24 models
> show #!22 models
> hide #!22 models
> volume #25 level 0.2164
> save CS_P10_J41_NU_sharp_flip.mrc #25
> close #25
> show #!24 models
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow1.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J255_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J255_002_volume_map_sharp.mrc as #25, grid size 80,80,80,
pixel 3.32, shown at level 0.649, step 1, values float32
> hide #!24 models
> volume flip #25
Opened cryosparc_P4_J255_002_volume_map_sharp.mrc z flip as #26, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #25
> rename CS_P4_J255_sharp_flip id #25
Missing or invalid "models" argument: invalid models specifier
> rename #26 CS_P4_J255_sharp_flip id #25
> save CS_P4_J255_sharp_flip.mrc #25
> show #!21 models
> hide #!21 models
> show #!24 models
> fitmap #25 inMap #24
Fit map CS_P4_J255_sharp_flip.mrc in map CS_P4_J176_NU_sharp_flip.mrc using
5116 points
correlation = 0.3392, correlation about mean = 0.06206, overlap = 2168
steps = 64, shift = 8.32, angle = 5.45 degrees
Position of CS_P4_J255_sharp_flip.mrc (#25) relative to
CS_P4_J176_NU_sharp_flip.mrc (#24) coordinates:
Matrix rotation and translation
-0.61720035 -0.75989860 -0.20400451 353.05950420
0.73150715 -0.64968488 0.20689815 96.93395715
-0.28976026 -0.02153315 0.95685700 43.12583281
Axis -0.15115555 0.05674554 0.98687990
Axis point 157.34041998 128.70985965 0.00000000
Rotation angle (degrees) 130.92072050
Shift along axis -5.30631665
> ui mousemode right "rotate selected models"
> select add #25
2 models selected
> view matrix models
> #25,-0.47042,-0.83357,-0.28961,363.38,0.84754,-0.51818,0.11478,76.044,-0.24575,-0.19146,0.95024,72.926
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.47042,-0.83357,-0.28961,355.09,0.84754,-0.51818,0.11478,66.81,-0.24575,-0.19146,0.95024,74.95
> view matrix models
> #25,-0.47042,-0.83357,-0.28961,355.15,0.84754,-0.51818,0.11478,66.803,-0.24575,-0.19146,0.95024,74.561
> fitmap #25 inMap #24
Fit map CS_P4_J255_sharp_flip.mrc in map CS_P4_J176_NU_sharp_flip.mrc using
5116 points
correlation = 0.8943, correlation about mean = 0.6059, overlap = 8709
steps = 84, shift = 8.95, angle = 14.5 degrees
Position of CS_P4_J255_sharp_flip.mrc (#25) relative to
CS_P4_J176_NU_sharp_flip.mrc (#24) coordinates:
Matrix rotation and translation
-0.48869161 0.86324945 -0.12641554 102.63693670
-0.86157381 -0.50031742 -0.08586638 328.42188396
-0.13737200 0.06695414 0.98825405 11.50507804
Axis 0.08825319 0.00632731 -0.99607798
Axis point 146.96136624 134.50878130 0.00000000
Rotation angle (degrees) 120.02497766
Shift along axis -0.32389146
> select subtract #25
Nothing selected
> save CS_P4_J255_sharp_flip.mrc #25
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J256_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J256_003_volume_map_sharp.mrc as #26, grid size 80,80,80,
pixel 3.32, shown at level 1.01, step 1, values float32
> hide #!25 models
> hide #!24 models
> select add #26
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.89385,-0.39986,0.20284,290.33,-0.34063,0.89978,0.2727,28.49,-0.29155,0.17466,-0.94047,242.77
> select subtract #26
Nothing selected
> show #!25 models
> fitmap #26 inMap #25
Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc in map
CS_P4_J255_sharp_flip.mrc using 5120 points
correlation = 0.5232, correlation about mean = 0.0553, overlap = 3214
steps = 120, shift = 25.3, angle = 15.3 degrees
Position of cryosparc_P4_J256_003_volume_map_sharp.mrc (#26) relative to
CS_P4_J255_sharp_flip.mrc (#25) coordinates:
Matrix rotation and translation
-0.15531756 0.84438274 0.51273214 -19.64184672
0.98713928 0.15254692 0.04780678 -29.86548711
-0.03784849 0.51356326 -0.85721658 167.46829582
Axis 0.63355180 0.74893504 0.19418658
Axis point 24.16142457 0.00000000 89.91884511
Rotation angle (degrees) 158.43381860
Shift along axis -2.29134077
> select add #26
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.87857,-0.47692,-0.025855,314.85,-0.44818,0.80449,0.38978,38.161,-0.16509,0.35404,-0.92054,233.61
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.93629,-0.25688,0.23952,260.92,-0.23661,0.96532,0.11035,19.606,-0.25956,0.046645,-0.9646,294.56
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.93629,-0.25688,0.23952,186.31,-0.23661,0.96532,0.11035,26.555,-0.25956,0.046645,-0.9646,285.53
> select subtract #26
Nothing selected
> volume flip #26
Opened cryosparc_P4_J256_003_volume_map_sharp.mrc z flip as #27, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #26
> select add #27
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #27,-0.91261,-0.40844,0.017647,236.5,0.22697,-0.47029,0.85283,55.691,-0.34003,0.78231,0.5219,-22.328
> view matrix models
> #27,-0.9144,-0.40478,0.0045882,238.13,0.22235,-0.49276,0.84128,61.136,-0.33827,0.77029,0.54058,-23.608
> view matrix models
> #27,-0.50015,0.79795,-0.33634,63.369,-0.80597,-0.57099,-0.15615,357.35,-0.31664,0.19298,0.92871,-2.4372
> ui mousemode right "translate selected models"
> view matrix models
> #27,-0.50015,0.79795,-0.33634,139.66,-0.80597,-0.57099,-0.15615,346.55,-0.31664,0.19298,0.92871,33.757
> fitmap #27 inMap #25
Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc z flip in map
CS_P4_J255_sharp_flip.mrc using 5120 points
correlation = 0.5523, correlation about mean = 0.08213, overlap = 3668
steps = 72, shift = 2.85, angle = 5.49 degrees
Position of cryosparc_P4_J256_003_volume_map_sharp.mrc z flip (#27) relative
to CS_P4_J255_sharp_flip.mrc (#25) coordinates:
Matrix rotation and translation
-0.50078193 -0.83716343 -0.21994286 353.70374510
0.81104417 -0.54259583 0.21862553 68.19134780
-0.30236538 -0.06889966 0.95069870 54.62167416
Axis -0.17164375 0.04920372 0.98392958
Axis point 162.79794553 129.91438640 0.00000000
Rotation angle (degrees) 123.11624986
Shift along axis -3.61188964
> view matrix models
> #27,-0.56613,0.75777,-0.32448,155.66,-0.74832,-0.63753,-0.18323,351.66,-0.34571,0.13908,0.92798,47.028
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.96274,0.27031,-0.0085132,-30.789,-0.27044,0.96237,-0.026732,40.459,0.00096683,0.028039,0.99961,4.8234
> fitmap #27 inMap #25
Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc z flip in map
CS_P4_J255_sharp_flip.mrc using 5120 points
correlation = 0.9111, correlation about mean = 0.5876, overlap = 9195
steps = 60, shift = 4.49, angle = 4.9 degrees
Position of cryosparc_P4_J256_003_volume_map_sharp.mrc z flip (#27) relative
to CS_P4_J255_sharp_flip.mrc (#25) coordinates:
Matrix rotation and translation
-0.48877401 0.86149397 -0.13757950 104.57166396
-0.86119668 -0.50165763 -0.08173068 327.97179743
-0.13942829 0.07853517 0.98711295 10.19538079
Axis 0.09263223 0.00106859 -0.99569982
Axis point 147.63593381 133.73777093 0.00000000
Rotation angle (degrees) 120.10984192
Shift along axis -0.11436514
> select subtract #27
Nothing selected
> hide #!25 models
> rename #27 CS_P4_J256_sharp_flip id #26
> save CS_P4_J256_sharp_flip.mrc #26
> show #!25 models
> hide #!25 models
> hide #!26 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J257_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J257_002_volume_map_sharp.mrc as #27, grid size 80,80,80,
pixel 3.32, shown at level 0.915, step 1, values float32
> select add #27
2 models selected
> show #!26 models
> view matrix models
> #27,0.43348,0.88304,0.17982,-64.533,0.89699,-0.44198,0.0081618,72.887,0.086685,0.15776,-0.98367,205.49
> hide #!26 models
> select subtract #27
Nothing selected
> volume flip #27
Opened cryosparc_P4_J257_002_volume_map_sharp.mrc z flip as #28, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #27
> select add #28
2 models selected
> show #!26 models
> view matrix models
> #28,0.0384,0.0015757,0.99926,-5.8546,0.92609,-0.37568,-0.034996,65.933,0.37535,0.92675,-0.015886,-77.078
> view matrix models
> #28,0.75378,0.65514,-0.051086,-44.642,-0.54582,0.58092,-0.60384,218.55,-0.36592,0.48304,0.79547,-29.499
> view matrix models
> #28,0.93053,0.32568,-0.16747,-7.3436,-0.34314,0.93516,-0.087963,68.823,0.12796,0.13932,0.98195,-76.969
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.93053,0.32568,-0.16747,-12.031,-0.34314,0.93516,-0.087963,69.72,0.12796,0.13932,0.98195,-23.264
> select subtract #28
Nothing selected
> fitmap #28 inMap #26
Fit map cryosparc_P4_J257_002_volume_map_sharp.mrc z flip in map
CS_P4_J256_sharp_flip.mrc using 5113 points
correlation = 0.961, correlation about mean = 0.8355, overlap = 1.813e+04
steps = 76, shift = 3.44, angle = 10.7 degrees
Position of cryosparc_P4_J257_002_volume_map_sharp.mrc z flip (#28) relative
to CS_P4_J256_sharp_flip.mrc (#26) coordinates:
Matrix rotation and translation
0.99983973 0.00266136 0.01770477 -3.60430289
-0.00275366 0.99998275 0.00519130 -0.72993632
-0.01769065 -0.00523922 0.99982979 3.00234542
Axis -0.27967225 0.94905354 -0.14519233
Axis point 166.73187411 0.00000000 206.99324341
Rotation angle (degrees) 1.06849905
Shift along axis -0.12064266
> rename #28 CS_P4_J257_sharp_flip id #27
> save CS_P4_J257_sharp_flip.mrc #27
> hide #!26 models
> hide #!27 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J258_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J258_002_volume_map_sharp.mrc as #28, grid size 80,80,80,
pixel 3.32, shown at level 0.533, step 1, values float32
> select add #28
2 models selected
> show #!27 models
> view matrix models #28,1,0,0,2.9293,0,1,0,12.799,0,0,1,30.196
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.94564,-0.32466,0.018849,316.84,-0.32175,0.94244,0.090998,54.708,-0.047307,0.079987,-0.99567,265.03
> select up
56 models selected
> select up
56 models selected
> select down
2 models selected
> select down
2 models selected
> select subtract #28
Nothing selected
> hide #!27 models
> volume flip #28
Opened cryosparc_P4_J258_002_volume_map_sharp.mrc z flip as #29, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #28
> select add #29
2 models selected
> view matrix models
> #29,0.95822,0.27409,-0.081793,-16.892,-0.27702,0.96049,-0.026814,62.796,0.071212,0.048352,0.99629,-31.428
> show #!27 models
> select subtract #29
Nothing selected
> fitmap #29 inMap #27
Fit map cryosparc_P4_J258_002_volume_map_sharp.mrc z flip in map
CS_P4_J257_sharp_flip.mrc using 5117 points
correlation = 0.4043, correlation about mean = 0.1105, overlap = 1145
steps = 104, shift = 9.56, angle = 9.45 degrees
Position of cryosparc_P4_J258_002_volume_map_sharp.mrc z flip (#29) relative
to CS_P4_J257_sharp_flip.mrc (#27) coordinates:
Matrix rotation and translation
0.98218261 0.18784329 -0.00567361 -27.82492616
-0.18685004 0.97932905 0.07747035 28.59524537
0.02010861 -0.07502992 0.99697851 -24.36927466
Axis -0.37621012 -0.06360338 -0.92434872
Axis point 152.56947582 100.16313614 0.00000000
Rotation angle (degrees) 11.69370116
Shift along axis 31.17497259
> select add #29
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.91472,0.40193,-0.041674,-52.044,-0.39883,0.91458,0.066882,60.074,0.064997,-0.044558,0.99689,0.70588
> view matrix models
> #29,0.91472,0.40193,-0.041674,-39.705,-0.39883,0.91458,0.066882,54.066,0.064997,-0.044558,0.99689,6.2725
> fitmap #29 inMap #27
Fit map cryosparc_P4_J258_002_volume_map_sharp.mrc z flip in map
CS_P4_J257_sharp_flip.mrc using 5117 points
correlation = 0.8335, correlation about mean = 0.5457, overlap = 5135
steps = 64, shift = 1.52, angle = 12.1 degrees
Position of cryosparc_P4_J258_002_volume_map_sharp.mrc z flip (#29) relative
to CS_P4_J257_sharp_flip.mrc (#27) coordinates:
Matrix rotation and translation
0.99996433 -0.00752131 -0.00383843 1.74823892
0.00752090 0.99997170 -0.00012121 -0.88867123
0.00383923 0.00009234 0.99999262 -0.68815928
Axis 0.01264381 -0.45457780 0.89061729
Axis point 130.32470586 232.13443622 0.00000000
Rotation angle (degrees) 0.48385831
Shift along axis -0.18681194
> select subtract #29
Nothing selected
> rename #29 CS_P4_J258_sharp_flip id #28
> save CS_P4_J258_sharp_flip.mrc #28
> hide #!27 models
> hide #!28 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J259_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J259_002_volume_map_sharp.mrc as #29, grid size 80,80,80,
pixel 3.32, shown at level 0.567, step 1, values float32
> select add #29
2 models selected
> show #!28 models
> view matrix models #29,1,0,0,-4.0284,0,1,0,3.9973,0,0,1,26.374
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.37373,0.91624,0.14434,-63.019,0.92743,-0.36674,-0.073343,74.867,-0.014266,0.16128,-0.98681,258.72
> view matrix models
> #29,0.2129,0.93735,0.27578,-60.698,0.97539,-0.1873,-0.11636,49.108,-0.057419,0.29377,-0.95415,242.23
> hide #!28 models
> select subtract #29
Nothing selected
> volume flip #29
Opened cryosparc_P4_J259_002_volume_map_sharp.mrc z flip as #30, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #29
> select add #30
2 models selected
> show #!28 models
> view matrix models
> #30,0.90176,0.31537,-0.29559,8.3185,-0.32745,0.94483,0.0091223,54.046,0.28216,0.088565,0.95527,-34.506
> select subtract #30
Nothing selected
> fitmap #30 inMap #28
Fit map cryosparc_P4_J259_002_volume_map_sharp.mrc z flip in map
CS_P4_J258_sharp_flip.mrc using 5112 points
correlation = 0.9666, correlation about mean = 0.6628, overlap = 3020
steps = 80, shift = 5.99, angle = 15.1 degrees
Position of cryosparc_P4_J259_002_volume_map_sharp.mrc z flip (#30) relative
to CS_P4_J258_sharp_flip.mrc (#28) coordinates:
Matrix rotation and translation
0.99996699 0.00262374 -0.00768921 0.94371527
-0.00261765 0.99999625 0.00080251 0.08556771
0.00769129 -0.00078235 0.99997011 -0.47262490
Axis -0.09707497 -0.94207663 -0.32104217
Axis point 62.77947672 0.00000000 122.20423531
Rotation angle (degrees) 0.46771540
Shift along axis -0.02048995
> rename #30 CS_P4_J259_sharp_flip id #29
> save CS_P4_J259_sharp_flip.mrc #29
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow.cxs"
> hide #!29 models
> hide #!28 models
> show #!25 models
> color #25 #FCEDFF
> hide #!25 models
> show #!28 models
> color #28 #FCEDFF
> hide #!28 models
> show #!29 models
> color #29 #FCEDFF
> hide #!29 models
> show #!29 models
> show #!26 models
> hide #!29 models
> color #26 #99BFE5
> hide #!26 models
> show #!27 models
> color #27 #99BFE5
> view P1
> hide #!27 models
> show #!25 models
> ui mousemode right "translate selected models"
> ui mousemode right translate
> view P1
> save CS_P4_J255_NU_sharp.png supersample 3 transparentBackground true
> hide #!25 models
> show #!26 models
> volume #26 level 1.012
> save CS_P4_J256_NU_sharp.png supersample 3 transparentBackground true
> hide #!26 models
> show #!27 models
> save CS_P4_J257_NU_sharp.png supersample 3 transparentBackground true
> hide #!27 models
> show #!28 models
> save CS_P4_J258_NU_sharp.png supersample 3 transparentBackground true
> hide #!28 models
> show #!29 models
> save CS_P4_J259_NU_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #30, grid size
320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J267_008_volume_map_sharp.mrc"
Opened cryosparc_P4_J267_008_volume_map_sharp.mrc as #31, grid size
320,320,320, pixel 0.831, shown at level 0.0747, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J277_008_volume_map_sharp.mrc"
Opened cryosparc_P4_J277_008_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0762, step 2, values float32
> hide #!29 models
> hide #!30 models
> hide #!31 models
> show #!31 models
> hide #!32 models
> show #!30 models
> close #30
> show #!27 models
> select add #31
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #31,-0.90396,0.26529,0.33537,196.37,0.29187,0.95597,0.030503,-41.724,-0.31251,0.12546,-0.94159,315.51
> hide #!27 models
> view matrix models
> #31,-0.95736,-0.095902,0.27253,266.49,-0.06692,0.99125,0.11374,-5.5307,-0.28105,0.090649,-0.9554,317.94
> show #!29 models
> hide #!29 models
> select subtract #31
Nothing selected
> close #32
> volume flip #31
Opened cryosparc_P4_J267_008_volume_map_sharp.mrc z flip as #30, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> close #30
> show #!31 models
> select add #31
2 models selected
> show #!27 models
> ui mousemode right "translate selected models"
> view matrix models
> #31,-0.95736,-0.095902,0.27253,258.1,-0.06692,0.99125,0.11374,14.401,-0.28105,0.090649,-0.9554,295.97
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.57983,0.79903,0.15922,-85.975,0.81408,-0.57604,-0.073785,139.64,0.032763,0.1724,-0.98448,241.38
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.57983,0.79903,0.15922,-74.26,0.81408,-0.57604,-0.073785,114.14,0.032763,0.1724,-0.98448,243.66
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.38773,0.91358,0.12259,-56.869,0.92165,-0.3821,-0.067497,68.753,-0.014823,0.13915,-0.99016,256.48
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.38773,0.91358,0.12259,-59.17,0.92165,-0.3821,-0.067497,73.776,-0.014823,0.13915,-0.99016,255.81
> fitmap #31 inMap #27
Fit map cryosparc_P4_J267_008_volume_map_sharp.mrc in map
CS_P4_J257_sharp_flip.mrc using 40948 points
correlation = 0.4368, correlation about mean = 0.04808, overlap = 2838
steps = 84, shift = 6.03, angle = 16 degrees
Position of cryosparc_P4_J267_008_volume_map_sharp.mrc (#31) relative to
CS_P4_J257_sharp_flip.mrc (#27) coordinates:
Matrix rotation and translation
-0.09805932 0.98945486 0.10659935 2.84911711
0.99008140 0.10782511 -0.09006967 -2.59568012
-0.10061396 0.09670986 -0.99021412 262.50076525
Axis 0.66953234 0.74277951 0.00224590
Axis point 14.97851108 -0.00000000 131.13786872
Rotation angle (degrees) 171.98194915
Shift along axis 0.56910865
> select subtract #31
Nothing selected
> hide #!31 models
> hide #!27 models
> show #!31 models
> close #31
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J267_008_volume_map_sharp.mrc"
Opened cryosparc_P4_J267_008_volume_map_sharp.mrc as #30, grid size
320,320,320, pixel 0.831, shown at level 0.0747, step 2, values float32
> select add #30
2 models selected
> show #!27 models
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.59059,-0.80637,-0.031153,183.8,-0.80688,-0.59066,-0.008015,354.56,-0.011937,0.02987,-0.99948,293.1
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.59059,-0.80637,-0.031153,187.84,-0.80688,-0.59066,-0.008015,342.67,-0.011937,0.02987,-0.99948,267.57
> hide #!27 models
> show #!27 models
> hide #!30 models
> hide #!27 models
> show #!30 models
> volume flip #30
Opened cryosparc_P4_J267_008_volume_map_sharp.mrc z flip as #31, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> select subtract #30
Nothing selected
> close #30
> select add #31
2 models selected
> show #!27 models
> view matrix models
> #31,0.59059,-0.80637,-0.031153,181.08,-0.80688,-0.59066,-0.008015,342.68,-0.011937,0.02987,-0.99948,285.6
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.49825,-0.85813,0.12394,182.63,-0.032454,0.12438,0.9917,19.314,-0.86642,-0.49814,0.034125,354.11
> view matrix models
> #31,-0.47795,-0.87619,-0.061991,343.39,0.85267,-0.47976,0.20686,70.492,-0.21099,0.046011,0.9764,77.316
> ui mousemode right "translate selected models"
> view matrix models
> #31,-0.47795,-0.87619,-0.061991,322.39,0.85267,-0.47976,0.20686,71.691,-0.21099,0.046011,0.9764,36.515
> view matrix models
> #31,-0.47795,-0.87619,-0.061991,329.78,0.85267,-0.47976,0.20686,58.248,-0.21099,0.046011,0.9764,36.244
> fitmap #31 inMap #27
Fit map cryosparc_P4_J267_008_volume_map_sharp.mrc z flip in map
CS_P4_J257_sharp_flip.mrc using 327854 points
correlation = 0.6967, correlation about mean = 0.2684, overlap = 4.49e+04
steps = 92, shift = 8.63, angle = 16.2 degrees
Position of cryosparc_P4_J267_008_volume_map_sharp.mrc z flip (#31) relative
to CS_P4_J257_sharp_flip.mrc (#27) coordinates:
Matrix rotation and translation
-0.48810574 -0.85845883 -0.15748400 338.09346066
0.86132304 -0.50293557 0.07196129 74.97027819
-0.14098011 -0.10051988 0.98489611 32.48936744
Axis -0.09978729 -0.00954816 0.99496298
Axis point 149.01931346 135.27108975 0.00000000
Rotation angle (degrees) 120.20349080
Shift along axis -2.12754240
> select subtract #31
Nothing selected
> volume #27 level 1.164
> volume #31 level 0.1055
> hide #!27 models
> volume #31 level 0.1343
> color #31 #99BFE5
> rename #31 CS_P4_J267_sharp_flip id #30
> save CS_P4_J267_sharp_flip.mrc #30
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J277_008_volume_map_sharp.mrc"
Opened cryosparc_P4_J277_008_volume_map_sharp.mrc as #31, grid size
320,320,320, pixel 0.831, shown at level 0.0762, step 2, values float32
> hide #!30 models
> select add #31
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.50169,-0.77701,0.38022,112.38,-0.8444,-0.53533,0.020189,301.01,0.18786,-0.33119,-0.92467,273.22
> view matrix models
> #31,0.77218,-0.62718,0.10187,94.664,-0.63536,-0.764,0.11236,288.83,0.0073633,-0.15149,-0.98843,283.82
> volume flip #31
Opened cryosparc_P4_J277_008_volume_map_sharp.mrc z flip as #32, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> close #31
> select add #32
2 models selected
> show #!30 models
> view matrix models
> #32,0.90608,0.27127,-0.3247,15.596,-0.28323,0.95899,0.010829,28.44,0.31432,0.082155,0.94575,-47.16
> view matrix models
> #32,0.99239,-0.018676,-0.12173,15.559,0.019459,0.9998,0.0052468,-15.401,0.1216,-0.0075755,0.99255,-16.612
> ui mousemode right "translate selected models"
> view matrix models
> #32,0.99239,-0.018676,-0.12173,21.14,0.019459,0.9998,0.0052468,-2.6957,0.1216,-0.0075755,0.99255,-9.4459
> fitmap #32 inMap #30
Fit map cryosparc_P4_J277_008_volume_map_sharp.mrc z flip in map
CS_P4_J267_sharp_flip.mrc using 327711 points
correlation = 0.7196, correlation about mean = 0.3385, overlap = 5671
steps = 204, shift = 3.68, angle = 13.7 degrees
Position of cryosparc_P4_J277_008_volume_map_sharp.mrc z flip (#32) relative
to CS_P4_J267_sharp_flip.mrc (#30) coordinates:
Matrix rotation and translation
-0.48144357 0.86501463 -0.14128627 103.86408789
-0.86432037 -0.49531179 -0.08727288 328.52215562
-0.14547307 0.08009963 0.98611442 10.75546195
Axis 0.09633390 0.00240978 -0.99534616
Axis point 148.32654443 133.96556119 0.00000000
Rotation angle (degrees) 119.69088439
Shift along axis 0.09189113
> select subtract #32
Nothing selected
> volume #32 level 0.1306
> hide #!30 models
> volume #32 level 0.1432
> color #32 #99BFE5
> rename #32 CS_P4_J277_sharp_flip id #31
> save CS_P4_J277_sharp_flip.mrc #31
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32
> hide #!31 models
> select add #32
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #32,0.30706,0.95043,0.049005,-33.318,0.9497,-0.30268,-0.080397,47.411,-0.061579,0.071226,-0.99556,261.24
> volume flip #32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #33, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> show #!31 models
> show #!32 models
> view matrix models
> #32,0.19586,0.82677,-0.52734,72.951,0.95192,-0.28947,-0.10029,48.053,-0.23556,-0.48235,-0.84371,334.74
> view matrix models
> #32,0.038463,0.98737,0.15371,-15.568,0.97818,-0.0057722,-0.20769,22.74,-0.20418,0.15835,-0.96604,265.55
> close #32
> select add #33
2 models selected
> view matrix models
> #33,-0.36526,-0.91739,-0.15805,324.89,0.9276,-0.34439,-0.14472,64.223,0.078335,-0.19947,0.97677,17.619
> view matrix models
> #33,-0.3296,-0.92737,-0.17708,323.89,0.91639,-0.35937,0.17633,25.386,-0.22716,-0.10416,0.96827,47.503
> select subtract #33
Nothing selected
> fitmap #33 inMap #31
Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map
CS_P4_J277_sharp_flip.mrc using 327344 points
correlation = 0.3754, correlation about mean = 0.04431, overlap = 1099
steps = 64, shift = 4.4, angle = 1.24 degrees
Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative
to CS_P4_J277_sharp_flip.mrc (#31) coordinates:
Matrix rotation and translation
-0.52307807 -0.83656982 -0.16291178 338.77635518
0.81824450 -0.54640858 0.17864376 66.60900444
-0.23846438 -0.03985703 0.97033300 35.38091339
Axis -0.13076939 0.04521708 0.99038113
Axis point 153.51682890 124.48577590 0.00000000
Rotation angle (degrees) 123.33798629
Shift along axis -6.24912375
> volume #33 level 0.05666
> select add #33
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #33,-0.32295,-0.92807,-0.18543,326.53,0.9135,-0.3569,0.19529,26.322,-0.24742,-0.10632,0.96306,60.406
> fitmap #33 inMap #31
Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map
CS_P4_J277_sharp_flip.mrc using 194771 points
correlation = 0.7316, correlation about mean = 0.2783, overlap = 2429
steps = 104, shift = 3.72, angle = 6.69 degrees
Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative
to CS_P4_J277_sharp_flip.mrc (#31) coordinates:
Matrix rotation and translation
-0.48329817 -0.86312458 -0.14641999 335.54076959
0.86340511 -0.49758655 0.08330200 72.08568886
-0.14475663 -0.08616006 0.98570885 33.43360614
Axis -0.09768239 -0.00095880 0.99521718
Axis point 148.43445219 133.71191357 0.00000000
Rotation angle (degrees) 119.84054702
Shift along axis 0.42815717
> select subtract #33
Nothing selected
> select add #33
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #33,-0.6364,0.75107,-0.17577,140.89,-0.74512,-0.6575,-0.11171,345.32,-0.19948,0.059876,0.97807,29.849
> ui mousemode right "translate selected models"
> view matrix models
> #33,-0.6364,0.75107,-0.17577,136.82,-0.74512,-0.6575,-0.11171,338.86,-0.19948,0.059876,0.97807,29.687
> ui mousemode right "rotate selected models"
> view matrix models
> #33,-0.73358,0.64738,-0.20678,168.84,-0.63708,-0.76101,-0.12246,339.46,-0.23664,0.041901,0.97069,38.344
> fitmap #33 inMap #31
Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map
CS_P4_J277_sharp_flip.mrc using 194771 points
correlation = 0.4346, correlation about mean = 0.05784, overlap = 1046
steps = 96, shift = 4.05, angle = 4.16 degrees
Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative
to CS_P4_J277_sharp_flip.mrc (#31) coordinates:
Matrix rotation and translation
-0.58502424 0.80932802 -0.05229508 107.72395607
-0.80221021 -0.58694418 -0.10934029 332.49911712
-0.11918646 -0.02201508 0.99262777 22.68232922
Axis 0.05406170 0.04141143 -0.99767852
Axis point 139.16943260 139.24984383 0.00000000
Rotation angle (degrees) 126.13361686
Shift along axis -3.03667024
> ui mousemode right "translate selected models"
> view matrix models
> #33,-0.7311,0.66788,-0.13939,159.58,-0.65889,-0.74418,-0.10984,339.55,-0.17709,0.011538,0.98413,33.11
> fitmap #33 inMap #31
Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map
CS_P4_J277_sharp_flip.mrc using 194771 points
correlation = 0.7261, correlation about mean = 0.2429, overlap = 2435
steps = 148, shift = 3.57, angle = 8.91 degrees
Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative
to CS_P4_J277_sharp_flip.mrc (#31) coordinates:
Matrix rotation and translation
-0.47691102 0.86730315 -0.14262219 103.16958211
-0.86637561 -0.49120809 -0.09004393 328.47939238
-0.14815256 0.08062145 0.98567285 11.48812128
Axis 0.09796714 0.00317460 -0.99518459
Axis point 148.54824739 133.97305983 0.00000000
Rotation angle (degrees) 119.42100612
Shift along axis -0.28278057
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.98687,0.16137,0.0076046,-28.356,-0.15803,0.97406,-0.16197,41.243,-0.033544,0.15864,0.98677,-7.5792
> ui mousemode right "translate selected models"
> view matrix models
> #33,0.98687,0.16137,0.0076046,-22.398,-0.15803,0.97406,-0.16197,51.235,-0.033544,0.15864,0.98677,-4.7399
> fitmap #33 inMap #31
Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map
CS_P4_J277_sharp_flip.mrc using 194771 points
correlation = 0.9896, correlation about mean = 0.9159, overlap = 4214
steps = 120, shift = 4.17, angle = 9.65 degrees
Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative
to CS_P4_J277_sharp_flip.mrc (#31) coordinates:
Matrix rotation and translation
0.99997973 -0.00439362 0.00460748 -0.02530815
0.00439161 0.99999024 0.00044636 -0.51759472
-0.00460939 -0.00042611 0.99998927 1.01725436
Axis -0.06835965 0.72216012 0.68833983
Axis point 171.68283436 0.00000000 1.37920014
Rotation angle (degrees) 0.36563312
Shift along axis 0.32816049
> select subtract #33
Nothing selected
> hide #!31 models
> show #!31 models
> hide #!31 models
> volume #33 level 0.06481
> color #33 #99BFE5
> view P1
> rename #33 CS_P4_J285_sharp_flip id #32
> save CS_P4_J285_sharp_flip.mrc #32
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow.cxs"
> save CS_P4_J285_NU_sharp.png supersample 3 transparentBackground true
> hide #!32 models
> show #!31 models
> save CS_P4_J277_NU_sharp.png supersample 3 transparentBackground true
> hide #!31 models
> show #!30 models
> save CS_P4_J267_NU_sharp.png supersample 3 transparentBackground true
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32
> select add #33
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.77382,-0.58736,0.23709,68.017,-0.6199,-0.77915,0.092993,287.71,0.13011,-0.21893,-0.96703,293.89
> volume flip sel
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #34, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> select subtract #33
Nothing selected
> select add #34
2 models selected
> view matrix models
> #34,0.96024,0.18105,-0.2125,4.9844,-0.18441,0.98284,0.0040821,22.146,0.20959,0.035266,0.97715,4.1522
> volume #34 level 0.06153
> ui mousemode right "translate selected models"
> view matrix models
> #34,0.96024,0.18105,-0.2125,5.3992,-0.18441,0.98284,0.0040821,24.944,0.20959,0.035266,0.97715,-19.851
> fitmap #34 inMap #30
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
CS_P4_J267_sharp_flip.mrc using 179913 points
correlation = 0.7668, correlation about mean = 0.2691, overlap = 2384
steps = 132, shift = 4.76, angle = 10.2 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative
to CS_P4_J267_sharp_flip.mrc (#30) coordinates:
Matrix rotation and translation
-0.47859383 0.86460690 -0.15297990 105.65226772
-0.86128787 -0.49615211 -0.10961884 331.90892973
-0.17067851 0.07929683 0.98213077 14.98614385
Axis 0.10880400 0.01019333 -0.99401096
Axis point 150.51207819 135.19673705 0.00000000
Rotation angle (degrees) 119.75601097
Shift along axis -0.01774616
> select subtract #34
Nothing selected
> select add #34
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #34,-0.29858,-0.92833,-0.22151,340.08,0.93935,-0.32688,0.10377,36.917,-0.16874,-0.17709,0.96962,60.484
> fitmap #34 inMap #30
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
CS_P4_J267_sharp_flip.mrc using 179913 points
correlation = 0.4184, correlation about mean = 0.03499, overlap = 815.8
steps = 72, shift = 3.19, angle = 2.56 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative
to CS_P4_J267_sharp_flip.mrc (#30) coordinates:
Matrix rotation and translation
0.99975679 -0.00914856 -0.02006678 -0.29483780
0.00937915 0.99989072 0.01142689 -12.23865962
0.01996005 -0.01161232 0.99973334 -0.12571505
Axis -0.46299067 -0.80436995 0.37232865
Axis point 194.44052306 0.00000000 212.15518455
Rotation angle (degrees) 1.42571524
Shift along axis 9.93410983
> ui mousemode right "translate selected models"
> view matrix models
> #34,-0.29149,-0.93644,-0.19523,323.34,0.9479,-0.31019,0.07257,35.755,-0.12852,-0.16391,0.97807,48.671
> fitmap #34 inMap #30
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
CS_P4_J267_sharp_flip.mrc using 179913 points
correlation = 0.9696, correlation about mean = 0.7683, overlap = 3705
steps = 76, shift = 2.39, angle = 2.68 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative
to CS_P4_J267_sharp_flip.mrc (#30) coordinates:
Matrix rotation and translation
0.99970034 -0.00006024 0.02447927 -4.11138943
0.00004629 0.99999984 0.00057062 0.05899118
-0.02447930 -0.00056932 0.99970018 3.40337319
Axis -0.02327752 0.99972667 0.00217546
Axis point 136.94050248 0.00000000 169.47617625
Rotation angle (degrees) 1.40308329
Shift along axis 0.16208189
> select subtract #34
Nothing selected
> hide #!30 models
> show #!32 models
> hide #!31 models
> volume #34 level 0.06805
> hide #!32 models
> view P1
> close #33
> rename #34 CS_P4_J282_sharp_flip id #33
> save CS_P4_J282_sharp_flip.mrc #33
> view P1
> save CS_P4_J282_NU_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow1.cxs"
> color #33 #99BFE5
> save CS_P4_J282_NU_sharp1.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow1.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J287_map_locres.mrc"
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 9.77, step 2, values float32
> rename #34 cryosparc_P4_J287_map_locres_forJ282
> select add #34
2 models selected
> view matrix models #34,1,0,0,-1.0935,0,1,0,0.90366,0,0,1,6.3532
> ui mousemode right "rotate selected models"
> view matrix models
> #34,0.41458,0.88648,0.20563,-71.892,0.90978,-0.4089,-0.07146,80.866,0.020734,0.2167,-0.97602,247.42
> view matrix models
> #34,0.40248,0.89866,0.17442,-67.589,0.91533,-0.39227,-0.091056,80.514,-0.013407,0.1963,-0.98045,255.56
> view matrix models
> #34,0.3547,0.92587,0.13022,-58.659,0.93218,-0.33944,-0.12576,75.687,-0.072238,0.166,-0.98348,268.27
> fitmap #34 inMap #33
Fit map cryosparc_P4_J287_map_locres_forJ282 in map CS_P4_J282_sharp_flip.mrc
using 40893 points
correlation = 0.2997, correlation about mean = 0.02148, overlap = 2955
steps = 140, shift = 9.61, angle = 2.61 degrees
Position of cryosparc_P4_J287_map_locres_forJ282 (#34) relative to
CS_P4_J282_sharp_flip.mrc (#33) coordinates:
Matrix rotation and translation
0.77162333 -0.63598985 0.01069393 118.29154644
-0.63440309 -0.76826072 0.08548800 317.77796206
-0.04615378 -0.07274879 -0.99628182 298.10083492
Axis -0.94106809 0.33808548 0.00943679
Axis point 0.00000000 186.80747823 142.52542945
Rotation angle (degrees) 175.17728056
Shift along axis -1.07117046
> volume #34 level 6.762
> view matrix models
> #34,0.42433,0.90126,0.087581,-65.663,0.89997,-0.40908,-0.15069,88.731,-0.099987,0.14276,-0.98469,281
> ui mousemode right "translate selected models"
> view matrix models
> #34,0.42433,0.90126,0.087581,-62.736,0.89997,-0.40908,-0.15069,86.303,-0.099987,0.14276,-0.98469,272.65
> view matrix models
> #34,0.42433,0.90126,0.087581,-62.591,0.89997,-0.40908,-0.15069,86.167,-0.099987,0.14276,-0.98469,272.2
> volume #34 level 6.762
> volume #34 level 6.47
> ui tool show "Surface Color"
> color sample #33.1 map #34 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> select subtract #34
Nothing selected
> hide #!34 models
> key red-white-blue :0.0 :20.4 :40.8 showTool true
> ui mousemode right "color key"
> key red-white-blue :0.0 :20.4 :40.8 white:
> key red:0.0 white:20.4 blue:40.8 white: white:
> key red:0.0 white:20.4 blue:40.8 white:
> key red-white-blue :0.0 :20.4 :40.8
> key red-white-blue :0 :2 :4 showTool true
> ui mousemode right "color key"
> key red-white-blue :0 :2 :4 white:
> key red:0 white:2 blue:4 white: white:
> color single #33.1
> color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> key red-white-blue :0 :2 :4 showTool true
> ui mousemode right "color key"
> key red-white-blue :0 :2 :4 showTool true
> key red-white-blue :0 :2 :4 white:
> key red:0 white:2 blue:4 white: white:
> key red:0 white:2 blue:4 white: white:0
> key red:0 white:2 blue:4 white:1 white:0
> key red:0 white:2 blue:2 white:1 white:0
> key red:0 white:3 blue:2 white:1 white:0
> key red:4 white:3 blue:2 white:1 white:0
> key gnbu :4 :3 :2 :1 :0
> key esmfold :4 :3 :2 :1 :0
> key dark2-5 :4 :3 :2 :1 :0
> key pastel1-5 :4 :3 :2 :1 :0
> key blues :4 :3 :2 :1 :0
> key accent-5 :4 :3 :2 :1 :0
> color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> color sample #33.1 map #34 palette 0,#0000ff:2,#7f7fff:4,#ffffff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> key blue:0 #7f7fff:2 white:4 showTool true
> ui mousemode right "color key"
> key blue:0 #7f7fff:2 white:4 showTool true
> key blue:0 #7f7fff:2 white:4 white:
> key blue:0 #7f7fff:2 white:4 white: white:
> color sample #33.1 map #34 palette
> 0,#0000ff:1,#7f7fff:2,#ffffff:3,#ff7f7f:4,#ff0000 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> key blue:0 #7f7fff:1 white:2 #ff7f7f:3 red:4 showTool true
> ui mousemode right "color key"
> color sample #33.1 map #34 palette
> 0,#0000ff:1,#7f7fff:2,#ffffff:3,#ff7f7f:4,#ff0000 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> color sample #33.1 map #34 palette
> 0,#ff0000:1,#ff7f7f:2,#ffffff:3,#7f7fff:4,#0000ff outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> color sample #33.1 map #34 palette
> 0,#ff0000:2,#ff7f7f:4,#ffffff:5,#7f7fff:8,#0000ff outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> volume #33 level 0.08574
> key red:0 #ff7f7f:2 white:4 #7f7fff:5 blue:8 showTool true
> key red:0 #ff7f7f:2 white:4 #7f7fff:6 blue:8 showTool true
> color sample #33.1 map #34 palette
> 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff7f7f:8,#ff0000 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> color sample #33.1 map #34 palette
> 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff7f7f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> key blue:0 #7f7fff:2 white:4 #ff7f7f:6 #fff6c0:8 showTool true
> color sample #33.1 map #34 palette
> 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ffad7f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> color sample #33.1 map #34 palette
> 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> key blue:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> color sample #33.1 map #34 palette
> 0,#fff6c0:2,#ff967f:4,#ffffff:6,#7f7fff:8,#0000ff outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> color sample #33.1 map #34 palette
> 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> key blue:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> color sample #33.1 map #34 palette
> 0,#00a7ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> key #00a7ff:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> color sample #33.1 map #34 palette
> 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow2.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J288_map_locres.mrc"
Opened cryosparc_P4_J288_map_locres.mrc as #36, grid size 320,320,320, pixel
0.831, shown at level 8.93, step 2, values float32
> hide #35 models
> show #35 models
> hide #!36 models
> hide #!33 models
> show #!33 models
> rename #36 cryosparc_P4_J288_map_locres_forJ285
> hide #!33 models
> show #!32 models
> hide #35 models
> show #!36 models
> select add #36
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.54984,-0.77769,0.30476,129.28,-0.81459,-0.57994,-0.010221,331.17,0.18469,-0.24264,-0.95237,263.23
> ui mousemode right "translate selected models"
> view matrix models
> #36,0.54984,-0.77769,0.30476,119.97,-0.81459,-0.57994,-0.010221,318.58,0.18469,-0.24264,-0.95237,280.96
> volume #36 level 6.234
> select subtract #36
Nothing selected
> ui tool show "Surface Color"
> color sample #32.1 map #36 palette
> 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> hide #!36 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!32 models
> show #!32 models
> hide #!33 models
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> show #!36 models
> hide #!36 models
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 white:
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8
Fetching compressed palette custom from
https://www.colourlovers.com/api/palettes?keywords=custom&format=json&numResults=100
Could not find palette custom at COLOURlovers.com using keyword search
> color sample #32.1 map #36 palette
> 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> hide #!32 models
> show #35 models
> show #!32 models
> select add #35
1 model selected
> view matrix models #35,1,0,0,-1.208,0,1,0,-1.3654,0,0,1,1.1486
> select subtract #35
Nothing selected
> select add #35
1 model selected
> select subtract #35
Nothing selected
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> ui mousemode right "color key"
> select add #35
1 model selected
> show #35
> view W35
Expected an objects specifier or a view name or a keyword
> view #35
No displayed objects specified.
> close #35
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> ui mousemode right "color key"
> hide #!32 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> volume #33 level 0.06991
> hide #!33 models
> show #!32 models
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow2.cxs"
> color sample #32.1 map #36 palette
> 0,#00a7ff:2,#99bfe5:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> key #00a7ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true
> ui mousemode right "color key"
> color sample #32.1 map #36 palette
> 0,#00a7ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#d2a5ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> key #d2a5ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true
> view #35
No objects specified.
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> key #e7c4ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow2.cxs"
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#99bfe5:4,#5da0ff:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#e0bfe8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#e0dee8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#e0dee8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#6676ed:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#6676ed:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#99bfe5:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#99bfe5:4,#6676ed:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#99bfe5:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#799bea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#5756ea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#ffdedd:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#ffc9a3:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> key #ffb17f:0 #527dea:2 #99bfe5:4 #fff6c0:6 #f4fff3:8 showTool true
> ui mousemode right "color key"
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow3.cxs"
> hide #!32 models
> show #!33 models
> hide #!33 models
> show #!32 models
> hide #!32 models
> show #!33 models
> hide #!33 models
> show #!32 models
> volume #34 step 1
> volume #36 step 1
> show #!36 models
> volume flip #36
Opened cryosparc_P4_J288_map_locres_forJ285 z flip as #38, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> hide #37 models
> ui mousemode right "rotate selected models"
> hide #!32 models
> show #!32 models
> hide #!38 models
> show #!38 models
> select add #38
2 models selected
> view matrix models
> #38,-0.22965,0.94651,-0.22667,61.099,-0.95753,-0.26145,-0.12161,309.34,-0.17437,0.18912,0.96635,13.289
> view matrix models
> #38,-0.47581,-0.84028,-0.25987,345.82,0.86453,-0.50117,0.037622,69.811,-0.16185,-0.20677,0.96491,66.334
> view matrix models
> #38,-0.72836,0.6263,-0.27792,180.88,-0.55109,-0.77649,-0.30556,349.01,-0.40718,-0.069403,0.91071,88.496
> view matrix models
> #38,-0.422,0.88275,-0.20657,93.707,-0.7937,-0.46985,-0.38638,351.04,-0.43814,0.0009021,0.89891,84.657
> fitmap #38 inMap #32
Fit map cryosparc_P4_J288_map_locres_forJ285 z flip in map
CS_P4_J285_sharp_flip.mrc using 1112104 points
correlation = 0.2781, correlation about mean = -0.02765, overlap = 7.665e+04
steps = 172, shift = 16.7, angle = 11.9 degrees
Position of cryosparc_P4_J288_map_locres_forJ285 z flip (#38) relative to
CS_P4_J285_sharp_flip.mrc (#32) coordinates:
Matrix rotation and translation
-0.15731459 0.96448973 -0.21215945 50.76791567
-0.83839054 -0.24396591 -0.48742375 323.17714111
-0.52187488 0.10119361 0.84699849 86.68679965
Axis 0.30630695 0.16117090 -0.93818974
Axis point 169.99659509 146.99779714 0.00000000
Rotation angle (degrees) 106.08964492
Shift along axis -13.69134858
> ui mousemode right "translate selected models"
> view matrix models
> #38,-0.29391,0.88572,-0.35933,106.9,-0.78003,-0.43953,-0.4454,363.34,-0.55243,0.14938,0.82006,93.87
> ui mousemode right "rotate selected models"
> volume #38 level 4.082
> view matrix models
> #38,-0.44764,0.81063,-0.37749,140.89,-0.70715,-0.57929,-0.40543,367.19,-0.54732,0.085454,0.83255,100.3
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models
> #38,-0.44764,0.81063,-0.37749,135.23,-0.70715,-0.57929,-0.40543,367.93,-0.54732,0.085454,0.83255,97.332
> view matrix models
> #38,-0.44764,0.81063,-0.37749,134.86,-0.70715,-0.57929,-0.40543,366.07,-0.54732,0.085454,0.83255,96.949
> select subtract #38
Nothing selected
> hide #!38 models
> color sample #32.1 map #38 palette
> 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.286, maximum 42.51
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/CS_P4_J282_sharp_flip.mrc"
Opened CS_P4_J282_sharp_flip.mrc as #39, grid size 320,320,320, pixel 0.831,
shown at level 0.0392, step 2, values float32
> hide #!32 models
> close #39
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #35, grid size
320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J287_map_locres.mrc"
Opened cryosparc_P4_J287_map_locres_forJ282 as #39, grid size 320,320,320,
pixel 0.831, shown at level 9.77, step 2, values float32
> volume #39 level 4.139
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J287_map_locres.mrc"
Opened cryosparc_P4_J287_map_locres_forJ282 as #40, grid size 320,320,320,
pixel 0.831, shown at level 9.77, step 2, values float32
> close #40
> color sample #35.1 map #39 palette
> 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.417, maximum 39.82
> hide #!39 models
> volume #35 step 1
> volume #35 level 0.06749
> color sample #35.1 map #39 palette
> 0,#ffb17f:1,#527dea:2,#99bfe5:3,#fff6c0:4,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 3.044, mean 3.567, maximum 40.68
> color sample #35.1 map #39 palette
> 0,#ffb17f:2,#527dea:3,#99bfe5:4,#fff6c0:5,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 3.044, mean 3.567, maximum 40.68
> color sample #35.1 map #39 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 3.044, mean 3.567, maximum 40.68
> close #32
> close #33
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow.cxs"
> close #39
> close #38
> close #36
> close #35
> show #!34 models
> hide #!34 models
> close #34
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J287_map_locres.mrc"
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 9.77, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J288_map_locres.mrc"
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 8.93, step 2, values float32
> rename #37 Color key id #36
Expected a keyword
> rename #37 Color_key id #36
Cannot change id of 2D overlay models (Color_key #37)
> hide #!33 models
> hide #!35 models
> volume #34 level 6.298
> volume #34 level 3.171
> volume #34 level 3.779
> hide #!34 models
> ui tool show "Surface Color"
No surface chosen for coloring
> show #!34 models
> hide #!34 models
> color sample #32.1 map #34 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.417, maximum 39.82
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
Could not find palette custom at COLOURlovers.com using keyword search
> show #37 models
> key pos 0.558738,0.385722 size 0.0255738,0.0868715
> key pos 0.723062,0.0751149
> key pos 0.862303,0.0795068
> key pos 0.846838,0.0779833
> select add #37
1 model selected
> key pos 0.819995,0.0796645
> key pos 0.812107,0.0767711
> key pos 0.825223,0.13099
> select subtract #37
Nothing selected
> undo
[Repeated 3 time(s)]
> color sample #32.1 map #34 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.417, maximum 39.82
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> show #37 models
> select add #37
1 model selected
> view matrix models
> #37,0.70959,0.62592,0.32358,0.61324,-0.29635,0.68175,-0.66888,-0.0021786,-0.63926,0.37874,0.66925,0.69431
> close #37
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> hide #!32 models
> show #!32 models
> volume #32 level 0.04587
> volume #32 level 0.04884
> key pos 0.437353,0.539212 size 0.000454748,0.0481037
> hide #36 models
> show #36 models
> close #36
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
[Repeated 1 time(s)]
> ui mousemode right "color key"
> ui mousemode right translate
> ui mousemode middle 'color key'
> key border false
> key border true
> key borderWidth 1.0
> key borderWidth 0.0
> key borderWidth 1.0
> key colorTreatment distinct
> key colorTreatment blended
> ui mousemode middle translate
> ui mousemode middle "color key"
> key borderColor #bfbfbf
> key borderColor default
> key borderColor #bfbfbf
> key borderColor #030303
> key borderColor #020202
> key borderColor #010202
> key borderColor black
> key labelColor #bfbfbf
> key labelColor default
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key fontSize 21
> key fontSize 22
> key fontSize 23
> key fontSize 24
> key bold true
> key italic true
> key italic false
> key numericLabelSpacing equal
> key numericLabelSpacing proportional
> key labelSide left/top
> key labelSide right/bottom
> key justification left
> key labelSide right/bottom
> key justification decimal
> key justification right
> key justification left
> key labelOffset 1.0
> key labelOffset 2.0
> key labelOffset 3.0
> key labelOffset 4.0
> key labelOffset 5.0
> key labelOffset 4.0
> key labelOffset 3.0
> key labelOffset 2.0
> key ticks true
> key ticks false
> key size 0.26000,0.05000
> key size 0.27000,0.05000
> key size 0.26000,0.05000
> key size 0.25000,0.05000
> key size 0.24000,0.05000
> key size 0.23000,0.05000
> key size 0.22000,0.05000
> key size 0.22000,0.04000
> key size 0.21000,0.04000
> key size 0.20000,0.04000
> key size 0.19000,0.04000
> key bold false
> key borderWidth 2.0
> key border false
> key border true
> key size 0.18000,0.04000
> key size 0.17000,0.04000
> key size 0.17000,0.03000
> key size 0.17000,0.02000
> key size 0.16000,0.02000
> key size 0.15000,0.02000
> key size 0.14000,0.02000
> key size 0.15000,0.02000
> key size 0.14000,0.02000
> key size 0.14000,0.01000
> key size 0.14000,0.02000
> key size 0.14000,0.01000
> key size 0.14000,0.02000
> key size 0.14000,0.03000
> key size 0.14000,0.04000
> key size 0.14000,0.03000
> key bold true
> save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true
> hide #!32 models
> show #!33 models
> show #!35 models
> volume #33 level 0.0299
> undo
> show #!35 models
> volume #35 level 3.774
> hide #!35 models
> color sample #33.1 map #35 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.383, maximum 41.2
> volume #33 level 0.03991
> volume #33 level 0.049
> volume #33 level 0.06811
> volume #33 level 0.05628
> volume #33 level 0.05719
> ui mousemode right translate
[Repeated 1 time(s)]
> select add #37
1 model selected
> ui mousemode right translate
> select subtract #37
Nothing selected
> view #33
> volume #33 level 0.05264
> volume #33 level 0.05082
> save CS_P4_J285_NU_sharp.png supersample 3 transparentBackground true
> save CS_P4_J285_locres_sharp.png supersample 3 transparentBackground true
> hide #!33 models
> show #!32 models
> volume #32 level 0.05478
> save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow1.cxs"
> show #!33 models
> hide #!33 models
> volume flip #32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #38, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> color sample #38.1 map #34 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.643, maximum 46.37
> select add #38
2 models selected
> select subtract #38
Nothing selected
> show #!34 models
> hide #!34 models
> show #!32 models
> select add #38
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #38,0.96218,0.27239,0.0026401,-33.277,0.27218,-0.96095,-0.049909,243.62,-0.011058,0.04874,-0.99875,256.5
> fitmap #38 inMap #32
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points
correlation = 0.3998, correlation about mean = 0.04433, overlap = 423.6
steps = 132, shift = 4.37, angle = 6.4 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative
to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates:
Matrix rotation and translation
0.98647244 0.16384860 0.00507628 -21.42824077
0.16385811 -0.98468453 -0.05955579 259.77996198
-0.00475960 0.05958193 -0.99821207 257.16545694
Axis 0.99660933 0.08227896 0.00007951
Axis point 0.00000000 126.91521003 132.48208787
Rotation angle (degrees) 176.57330142
Shift along axis 0.03928788
> select subtract #38
Nothing selected
> select add #38
2 models selected
> view matrix models
> #38,-0.55814,-0.81354,-0.1632,351.46,-0.79796,0.58019,-0.16319,187.27,0.22745,0.039147,-0.973,224.57
> ui mousemode right "translate selected models"
> view matrix models
> #38,-0.55814,-0.81354,-0.1632,337.55,-0.79796,0.58019,-0.16319,184.57,0.22745,0.039147,-0.973,224.6
> fitmap #38 inMap #32
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points
correlation = 0.4208, correlation about mean = 0.04628, overlap = 461.9
steps = 76, shift = 2.33, angle = 4.27 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative
to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates:
Matrix rotation and translation
-0.49732082 -0.85447621 -0.15014131 334.86076124
-0.83743504 0.51801846 -0.17423960 201.03033487
0.22665956 0.03908062 -0.97318968 225.34606158
Axis 0.49228130 -0.86954734 0.03932608
Axis point 210.12674218 0.00000000 138.36301119
Rotation angle (degrees) 167.48677512
Shift along axis -1.09772430
> select subtract #38
Nothing selected
> select add #38
2 models selected
> view matrix models
> #38,-0.49732,-0.85448,-0.15014,335.05,-0.83744,0.51802,-0.17424,201.05,0.22666,0.039081,-0.97319,225.03
> ui mousemode right "rotate selected models"
> view matrix models
> #38,-0.016367,0.99633,0.084023,-21.562,0.99914,0.013095,0.039355,-10.502,0.03811,0.084595,-0.99569,247.71
> ui mousemode right "translate selected models"
> view matrix models
> #38,-0.016367,0.99633,0.084023,-11.414,0.99914,0.013095,0.039355,-8.4507,0.03811,0.084595,-0.99569,248.91
> fitmap #38 inMap #32
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points
correlation = 0.4638, correlation about mean = 0.04825, overlap = 549.2
steps = 212, shift = 3.48, angle = 14 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative
to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates:
Matrix rotation and translation
-0.11733678 0.98529275 -0.12421864 36.78201449
0.98526620 0.13117004 0.10974943 -32.51895072
0.12442908 -0.10951079 -0.98616672 260.89985464
Axis -0.66139292 -0.75003960 -0.00008010
Axis point 18.21387939 0.00000000 132.49954907
Rotation angle (degrees) 170.45882216
Shift along axis 0.04223943
> select subtract #38
Nothing selected
> hide #!32 models
> color sample #38.1 map #34 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 3.043, mean 3.992, maximum 41.6
> show #!34 models
> volume flip #34
Opened cryosparc_P4_J287_map_locres.mrc z flip as #39, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> select add #39
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #39,0.92903,0.36038,-0.083822,-29.473,0.36808,-0.92323,0.1103,201.34,-0.037639,-0.13332,-0.99036,275.09
> show #!34 models
> fitmap #39 imapt #34
Expected a keyword
> fitmap #39 inMap #34
Fit map cryosparc_P4_J287_map_locres.mrc z flip in map
cryosparc_P4_J287_map_locres.mrc using 2056381 points
correlation = 0.8371, correlation about mean = 0.04941, overlap = 1.057e+08
steps = 612, shift = 15.2, angle = 38.8 degrees
Position of cryosparc_P4_J287_map_locres.mrc z flip (#39) relative to
cryosparc_P4_J287_map_locres.mrc (#34) coordinates:
Matrix rotation and translation
0.49975558 0.86379414 -0.06406286 -38.69544656
0.86380943 -0.49157793 0.11038297 66.86486459
0.06385627 -0.11050260 -0.99182234 270.06743869
Axis -0.86536171 -0.50114779 0.00005993
Axis point 0.00000000 54.63554700 132.55703766
Rotation angle (degrees) 172.66756182
Shift along axis -0.00743630
> select subtract #39
Nothing selected
> hide #!39 models
> show #!39 models
> select add #39
2 models selected
> hide #37 models
> hide #!38 models
> view matrix models
> #39,0.37237,-0.92808,0.0029165,218.26,-0.92659,-0.37195,-0.055474,318.12,0.052569,0.017955,-0.99846,254.69
> ui mousemode right "translate selected models"
> view matrix models
> #39,0.37237,-0.92808,0.0029165,208.8,-0.92659,-0.37195,-0.055474,313.9,0.052569,0.017955,-0.99846,255.36
> ui mousemode right "rotate selected models"
> view matrix models
> #39,0.66947,-0.74091,0.05349,135.56,-0.73453,-0.67101,-0.10103,334.54,0.11074,0.028346,-0.99344,245.27
> ui mousemode right "translate selected models"
> view matrix models
> #39,0.66947,-0.74091,0.05349,211.58,-0.73453,-0.67101,-0.10103,368.3,0.11074,0.028346,-0.99344,245.76
> view matrix models
> #39,0.66947,-0.74091,0.05349,241.5,-0.73453,-0.67101,-0.10103,381.69,0.11074,0.028346,-0.99344,243.08
> view matrix models
> #39,0.66947,-0.74091,0.05349,287.43,-0.73453,-0.67101,-0.10103,402.31,0.11074,0.028346,-0.99344,237.25
> ui mousemode right "rotate selected models"
> view matrix models
> #39,-0.41494,0.89077,-0.18535,241.42,0.8738,0.44692,0.19168,-11.043,0.25358,-0.082424,-0.9638,229.13
> view matrix models
> #39,0.99948,-0.019992,0.025148,145.79,-0.021975,-0.99645,0.081215,326.06,0.023435,-0.081726,-0.99638,264.88
> ui mousemode right "translate selected models"
> view matrix models
> #39,0.99948,-0.019992,0.025148,-4.0949,-0.021975,-0.99645,0.081215,259.26,0.023435,-0.081726,-0.99638,270.42
> select subtract #39
Nothing selected
> hide #!34 models
> color sample #38.1 map #34 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 3.043, mean 3.992, maximum 41.6
> hide #!39 models
> show #!38 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #40, grid size
320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32
> hide #!38 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J287_map_locres.mrc"
Opened cryosparc_P4_J287_map_locres.mrc as #41, grid size 320,320,320, pixel
0.831, shown at level 9.77, step 2, values float32
> volume flip #40
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #42, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #41
Opened cryosparc_P4_J287_map_locres.mrc z flip as #43, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> volume #43 level 4.042
> color sample #42.1 map #43 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.484, maximum 42.57
> hide #!43 models
> hide #!42 models
> show #!38 models
> show #!39 models
> show #!40 models
> show #!41 models
> show #!42 models
> show #!43 models
> close #43
> close #38
> close #42
> close #41
> close #40
> close #39
> close #37
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> hide #36 models
> volume flip #32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #34
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> volume flip #33
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #35
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> hide #!39 models
> hide #!40 models
> hide #!38 models
> color sample #37.1 map #38 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.731, maximum 41.43
> hide #!37 models
> show #!37 models
> hide #!37 models
> show #!39 models
> color sample #39.1 map #40 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.67, maximum 40.73
> volume #39 level 0.05082
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> show #36 models
> select add #36
1 model selected
> key pos 0.366468,0.16715
> key pos 0.360149,0.168599
> key labelColor #bfbfbf
> key labelColor default
> key labelColor #bfbfbf
> key labelColor white
> key labelColor default
> key ticks true
> key tickLength 8.0
> key tickThickness 3.0
> key tickThickness 2.0
> key tickThickness 1.0
> key tickLength 10.0
> key tickLength 8.0
> key tickThickness 2.0
> key tickThickness 1.0
> key tickThickness 0.0
> key tickThickness 1.0
> key tickThickness 2.0
> key ticks false
> key labelOffset -1.0
> key labelOffset -2.0
> key labelOffset -1.0
> key labelOffset 0.0
> key labelOffset 1.0
> key labelOffset 2.0
> key labelOffset 3.0
> key labelOffset 4.0
> view matrix models #36,1,0,0,-0.86321,0,1,0,-0.41592,0,0,1,0.9887
> select subtract #36
Nothing selected
> select add #36
1 model selected
> view matrix models #36,1,0,0,-99.598,0,1,0,-41.849,0,0,1,63.569
> view matrix models #36,1,0,0,-99.715,0,1,0,-41.895,0,0,1,63.621
> view matrix models #36,1,0,0,-102.61,0,1,0,-42.915,0,0,1,63.831
> view matrix models #36,1,0,0,-126.49,0,1,0,-56.195,0,0,1,105.79
> view matrix models #36,1,0,0,-152.42,0,1,0,-56.013,0,0,1,31.21
> view matrix models #36,1,0,0,-131.29,0,1,0,-47.985,0,0,1,24.738
> view matrix models #36,1,0,0,-121.36,0,1,0,-44.649,0,0,1,25.261
> view matrix models #36,1,0,0,-121.37,0,1,0,-44.69,0,0,1,25.567
> view matrix models #36,1,0,0,-123.18,0,1,0,-45.336,0,0,1,25.776
> close #36
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> key pos 0.377773,0.195303
> key pos 0.377554,0.185959
> key borderWidth 3.0
> key labelOffset 1.0
> key labelOffset 2.0
> key labelOffset 3.0
> key labelOffset 4.0
> key labelOffset 5.0
> key labelOffset 6.0
> key size 0.24000,0.05000
> key size 0.23000,0.05000
> key size 0.23000,0.04000
> key size 0.23000,0.03000
> key size 0.22000,0.03000
> key size 0.21000,0.03000
> key size 0.20000,0.03000
> key size 0.19000,0.03000
> key size 0.18000,0.03000
> key size 0.17000,0.03000
> key size 0.16000,0.03000
> key size 0.15000,0.03000
> key size 0.16000,0.03000
> key size 0.17000,0.03000
> key size 0.17000,0.04000
> key size 0.17000,0.05000
> key size 0.17000,0.04000
> key pos 0.36134,0.205524 size 0.0323267,0.199875
> key pos 0.375585,0.243532 size 0.000780577,0.00120384
> key pos 0.393081,0.282969 size 0,0
[Repeated 1 time(s)]
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> hide #!39 models
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> key pos 0.654167,0.35194 size 0.0389145,0.208023
> show #!39 models
> key pos 0.434243,0.168612 size 0.0379186,0.161115
> hide #41 models
> ui mousemode right "translate selected models"
> ui mousemode right translate
[Repeated 1 time(s)]
> select add #41
1 model selected
> select subtract #41
Nothing selected
> show #41 models
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right select
> select clear
> ui mousemode right rotate
> ui mousemode right translate
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
[Repeated 1 time(s)]
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right select
> select clear
> select add #41
1 model selected
> select clear
Drag select of 39 cryosparc_P4_J285_006_volume_map_sharp.mrc z flip
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> select clear
Drag select of 39 cryosparc_P4_J285_006_volume_map_sharp.mrc z flip
> ui mousemode right translate
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> select subtract #41
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right rotate
> ui mousemode right translate
> hide #!39 models
> show #!39 models
> ui mousemode right select
> select #39
2 models selected
> ui mousemode right rotate
> ui mousemode right translate
> select subtract #39
Nothing selected
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> hide #!39 models
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode left "color key"
> ui mousemode left rotate
> ui mousemode right 'color key'
> key pos 0.683937,0.290603 size 0.0366198,0.178803
> show #!39 models
> key pos 0.885363,0.663755 size 0.0185522,0.00687018
> ui mousemode right translate
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> key pos 0.768821,0.24433 size 0.0347996,0.266198
> key labelOffset 7.0
> key labelOffset 8.0
> key labelOffset 9.0
> hide #!39 models
> show #!37 models
> volume #37 level 0.06504
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow2.cxs"
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> key fontSize 25
> key fontSize 26
> key fontSize 27
> key fontSize 28
> key fontSize 29
> key fontSize 30
> key fontSize 31
> key fontSize 32
> key fontSize 33
> key fontSize 34
> key fontSize 35
> save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true
> hide #!37 models
> show #!39 models
> volume #39 level 0.06897
> volume #39 level 0.06638
> save CS_P4_J285_locres_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow2.cxs"
> hide #!39 models
> hide #41 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/CS_P4_J282_sharp_flip.mrc"
Opened CS_P4_J282_sharp_flip.mrc as #42, grid size 320,320,320, pixel 0.831,
shown at level 0.0392, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe University/19. Model Building/2. AcrF
> Project/2. Bound-form/SA-F_B1/Model/aligned_model_for_J282.pdb"
Chain information for aligned_model_for_J282.pdb #43
---
Chain | Description
A B C | No description available
> hide #!42 models
> select #43/BC
Nothing selected
> select #43/B, C
15672 atoms, 15966 bonds, 2068 residues, 1 model selected
> delete sel
> show #!42 models
> volume zone #42 nearAtoms #43/A
> color #43 #FFF6C0
> volume zone #42 nearAtoms #43/A distance 5
Expected a keyword
> color zone #42 near #43/A distance 5
> color zone #42 near #43/A distance 5 tran 50
Expected a keyword
> color zone #42 near #43/A distance 5 tran 50
Expected a keyword
> color #43 #FFF6C0
> color zone #42 near #43/A distance 5
> color #43 #FFF6C0 transparency 50
> color zone #42 near #43/A distance 5
> graphics silhouettes false
> lighting full
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> graphics silhouettes false
> color #42 #99bfe580 models
> hide #43 models
> transparency #42 50
> lighting soft
> volume #42 level 0.0232
> lighting soft
> close #42
> close #43
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_02_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #36, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_01_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.178, step 1, values float32
> close #36
> show #!9 models
> select add #42
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #42,0.026241,-0.92593,0.37678,198.52,-0.063177,0.37462,0.92502,-34.721,-0.99766,-0.048078,-0.048667,279.22
> ui mousemode right "translate selected models"
> view matrix models
> #42,0.026241,-0.92593,0.37678,198.7,-0.063177,0.37462,0.92502,-33.267,-0.99766,-0.048078,-0.048667,263
> fitmap #42 inMap #9
Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20960 points
correlation = 1, correlation about mean = 1, overlap = 1571
steps = 128, shift = 5.08, angle = 27.9 degrees
Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#42) relative
to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.99999999 -0.00010909 0.00000609 0.02020954
0.00010909 0.99999995 0.00031305 -0.06272325
-0.00000612 -0.00031305 0.99999995 0.03217050
Axis -0.94414385 0.01842055 0.32901836
Axis point 0.00000000 112.87704178 199.81299213
Rotation angle (degrees) 0.01899762
Shift along axis -0.00965143
> select subtract #42
Nothing selected
> select add #42
2 models selected
> fitmap #42 inMap #9
Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20960 points
correlation = 1, correlation about mean = 1, overlap = 1571
steps = 40, shift = 0.00318, angle = 0.00769 degrees
Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#42) relative
to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.99999999 -0.00011772 0.00012933 0.00283694
0.00011769 0.99999996 0.00026066 -0.05912201
-0.00012937 -0.00026064 0.99999996 0.04294746
Axis -0.83040251 0.41209275 0.37498166
Axis point 0.00000000 180.01203882 210.06369623
Rotation angle (degrees) 0.01798432
Shift along axis -0.01061505
> select subtract #42
Nothing selected
> hide #!9 models
> volume #42 level 0.2579
> color #42 #ffffb2ff models
> color #42 #ffffb280 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/CS_P4_J282_sharp_flip.mrc"
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0392, step 2, values float32
> volume #42 level 0.1954
> select add #42
2 models selected
> view matrix models
> #42,0.15189,-0.98482,-0.084022,248.42,-0.056394,-0.093504,0.99402,24.018,-0.98679,-0.14625,-0.069741,273.86
> volume #42 level 0.2537
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_03_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
> close #43
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_02_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.216, step 1, values float32
> select add #43
4 models selected
> view matrix models
> #42,0.15189,-0.98482,-0.084022,246.73,-0.056394,-0.093504,0.99402,-45.124,-0.98679,-0.14625,-0.069741,235.92,#43,1,0,0,-1.6882,0,1,0,-69.141,0,0,1,-37.947
> view matrix models
> #42,0.15189,-0.98482,-0.084022,237,-0.056394,-0.093504,0.99402,126.12,-0.98679,-0.14625,-0.069741,312.08,#43,1,0,0,-11.419,0,1,0,102.11,0,0,1,38.221
> select subtract #42
2 models selected
> view matrix models #43,1,0,0,-10.922,0,1,0,105.75,0,0,1,25.23
> ui mousemode right "rotate selected models"
> view matrix models
> #43,0.053361,-0.96815,-0.24461,270.41,-0.10024,-0.24891,0.96332,141.36,-0.99353,-0.026885,-0.11033,315.47
> ui mousemode right "translate selected models"
> view matrix models
> #43,0.053361,-0.96815,-0.24461,276.43,-0.10024,-0.24891,0.96332,50.344,-0.99353,-0.026885,-0.11033,257.37
> ui mousemode right "rotate selected models"
> view matrix models
> #43,0.25016,-0.91768,-0.30868,252.37,-0.0074281,-0.32063,0.94718,48.872,-0.96818,-0.23465,-0.087026,276.42
> ui mousemode right "translate selected models"
> view matrix models
> #43,0.25016,-0.91768,-0.30868,252.17,-0.0074281,-0.32063,0.94718,49.119,-0.96818,-0.23465,-0.087026,280.28
> view matrix models
> #43,0.25016,-0.91768,-0.30868,245.18,-0.0074281,-0.32063,0.94718,41.479,-0.96818,-0.23465,-0.087026,278.46
> view matrix models
> #43,0.25016,-0.91768,-0.30868,244.24,-0.0074281,-0.32063,0.94718,46.881,-0.96818,-0.23465,-0.087026,278.05
> select add #42
4 models selected
> select subtract #43
2 models selected
> view matrix models
> #42,0.15189,-0.98482,-0.084022,248.26,-0.056394,-0.093504,0.99402,10.768,-0.98679,-0.14625,-0.069741,272.27
> select subtract #42
Nothing selected
> color #36 #99BFE5
> hide #!42 models
> select add #43
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #43,0.073784,-0.55439,0.82898,66.918,0.0052521,0.83145,0.55558,-43.45,-0.99726,-0.036639,0.064259,236.72
> ui mousemode right "translate selected models"
> view matrix models
> #43,0.073784,-0.55439,0.82898,82.905,0.0052521,0.83145,0.55558,-39.115,-0.99726,-0.036639,0.064259,236.78
> select subtract #43
Nothing selected
> volume #36 level 0.0602
> select add #43
2 models selected
> view matrix models
> #43,0.073784,-0.55439,0.82898,84.941,0.0052521,0.83145,0.55558,-38.546,-0.99726,-0.036639,0.064259,236.53
> view matrix models
> #43,0.073784,-0.55439,0.82898,84.833,0.0052521,0.83145,0.55558,-38.074,-0.99726,-0.036639,0.064259,236.34
> volume #43 level 0.1902
> color #43 #b2b2ff80 models
> volume #43 level 0.2283
> select add #40
4 models selected
> select subtract #40
2 models selected
> select subtract #43
Nothing selected
> color #43 #ffffb280 models
> color #43 #b2b2ff80 models
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow3.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_cryosparc_P4_J243_003_volume_map_35_TMD_regions_resampled.mrc"
Opened
cryosparc_P4_cryosparc_P4_J243_003_volume_map_35_TMD_regions_resampled.mrc as
#44, grid size 80,80,80, pixel 3.32, shown at level 0.324, step 1, values
float32
> close #44
> save CS_P4_J282_show_mask_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow4.cxs"
——— End of log from Sun May 3 17:29:06 2026 ———
> view name session-start
opened ChimeraX session
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J295_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J295_006_volume_map_sharp.mrc as #44, grid size
320,320,320, pixel 0.831, shown at level 0.0361, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J296_map_locres.mrc"
Opened cryosparc_P4_J296_map_locres.mrc as #45, grid size 320,320,320, pixel
0.831, shown at level 8.66, step 2, values float32
> hide #!43 models
> hide #!36 models
> hide #!45 models
> show #!45 models
> hide #!45 models
> volume flip #44
Opened cryosparc_P4_J295_006_volume_map_sharp.mrc z flip as #46, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #45
Opened cryosparc_P4_J296_map_locres.mrc z flip as #47, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> close #45
> close #44
> rename #46 CS_P4_J295_sharp_flip id #44
> save CS_P4_J295_sharp_flip.mrc #44
> rename #47 CS_P4_J296_locres_flip id #45
> save CS_P4_J296_locres_flip.mrc #45
> ui tool show "Surface Color"
> hide #!45 models
> color sample #44.1 map #45 palette #ffb17f:#527dea:#99bfe5:#fff6c0:#f4fff3
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.132, maximum 48.35
> show #41 models
> volume #44 level 0.0515
> color sample #44.1 map #45 palette
> 1,#ffb17f:2,#527dea:3,#99bfe5:4,#fff6c0:5,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#ffb17f:3,#527dea:4,#ffb17f:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#527dea:3,#99bfe5:4,#ffb17f:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> key #527dea:2 #99bfe5:3 #ffb17f:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#527dea outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> key #f4fff3:2 #fff6c0:3 #ffb17f:4 #99bfe5:5 #527dea:6 showTool true
> ui mousemode right "color key"
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#527dd6 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#46a2de outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#4d8fde outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#94aec1 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#a78bc1 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#c1a77f outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#89b3c1 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> color sample #44.1 map #45 palette
> 2,#ffb17f:3,#2c98ee:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> save CS_P4_J295_locres_sharp.png supersample 3 transparentBackground true
Cell requested for row 0 is out of bounds for table with 6 rows! Resizing
table model.
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260505_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J300_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J300_005_volume_map_sharp.mrc as #46, grid size
320,320,320, pixel 0.831, shown at level 0.0375, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J301_map_locres.mrc"
Opened cryosparc_P4_J301_map_locres.mrc as #47, grid size 320,320,320, pixel
0.831, shown at level 9.68, step 2, values float32
> hide #!44 models
> hide #!47 models
> volume flip #46
Opened cryosparc_P4_J300_005_volume_map_sharp.mrc z flip as #48, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #47
Opened cryosparc_P4_J301_map_locres.mrc z flip as #49, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> close #46
> close #47
> rename #48 CS_P4_J300_sharp_flip id #46
> rename #49 CS_P4_J301_locres_flip id #47
> save CS_P4_J301_locres_flip.mrc #47
> save CS_P4_J300_sharp_flip.mrc #46
> color sample #46.1 map #47 palette
> 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.498, maximum 44.88
> hide #!47 models
> volume #46 level 0.03399
> volume #46 level 0.06962
> volume #46 level 0.05919
> save CS_P4_J300_locres_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260505_SA-F_B1_workflow.cxs"
——— End of log from Tue May 5 09:31:57 2026 ———
> view name session-start
opened ChimeraX session
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J302_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J302_002_volume_map_sharp.mrc as #48, grid size 80,80,80,
pixel 3.32, shown at level 0.658, step 1, values float32
> select add #48
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #48,0.064602,0.97911,0.19278,-26.266,0.98732,-0.034646,-0.1549,22.036,-0.14498,0.20034,-0.96894,229.94
> volume flip #48
Opened cryosparc_P4_J302_002_volume_map_sharp.mrc z flip as #49, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #48
> rename #49 rename
> rename #49 CS_P4_J302_sharp_flip id #48
> save CS_P4_J302_sharp_flip.mrc #48
> select add #48
2 models selected
> view matrix models
> #48,-0.56486,-0.82475,0.026783,324.58,0.77395,-0.54076,-0.32951,143.72,0.28625,-0.1654,0.94377,-52.222
> hide #41 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!45 models
> hide #!45 models
> show #!43 models
> hide #!43 models
> show #!39 models
> ui mousemode right "translate selected models"
> view matrix models
> #48,-0.56486,-0.82475,0.026783,319.51,0.77395,-0.54076,-0.32951,139.04,0.28625,-0.1654,0.94377,-3.8614
> view matrix models
> #48,-0.56486,-0.82475,0.026783,321.32,0.77395,-0.54076,-0.32951,140.03,0.28625,-0.1654,0.94377,-10.821
> fitmap $48 inmap #39
Missing or invalid "atomsOrMap" argument: invalid objects specifier
> fitmap #48 inMap #39
Fit map CS_P4_J302_sharp_flip.mrc in map
cryosparc_P4_J285_006_volume_map_sharp.mrc z flip using 5112 points
correlation = 0.3608, correlation about mean = 0.02111, overlap = 103.8
steps = 76, shift = 4.71, angle = 3.71 degrees
Position of CS_P4_J302_sharp_flip.mrc (#48) relative to
cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#39) coordinates:
Matrix rotation and translation
-0.54436883 -0.83749052 0.04766738 317.13056079
0.79848148 -0.53475206 -0.27652762 129.04232256
0.25707950 -0.11247150 0.95982304 -11.58663120
Axis 0.09898047 -0.12634523 0.98703584
Axis point 124.28808276 149.04371086 0.00000000
Rotation angle (degrees) 124.03152255
Shift along axis 3.64942894
> ui mousemode right "rotate selected models"
> view matrix models
> #48,-0.38435,0.91427,-0.12797,86.018,-0.92117,-0.38898,-0.012326,307,-0.061046,0.11314,0.9917,-2.8083
> fitmap #48 inMap #39
Fit map CS_P4_J302_sharp_flip.mrc in map
cryosparc_P4_J285_006_volume_map_sharp.mrc z flip using 5112 points
correlation = 0.623, correlation about mean = 0.1973, overlap = 254
steps = 104, shift = 5.55, angle = 8.62 degrees
Position of CS_P4_J302_sharp_flip.mrc (#48) relative to
cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#39) coordinates:
Matrix rotation and translation
-0.49090927 0.85957769 -0.14189522 105.36638005
-0.85910240 -0.50468247 -0.08508012 328.20339808
-0.14474501 0.08013591 0.98621858 12.70754555
Axis 0.09568836 0.00165051 -0.99540997
Axis point 147.88121154 133.69042072 0.00000000
Rotation angle (degrees) 120.31054935
Shift along axis -2.02517664
> select subtract #48
Nothing selected
> volume #48 level 0.8066
> hide #!48 models
> show #!48 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> volume #48 level 0.6121
> show #!24 models
> hide #!24 models
> color #48 #99BFE5
> hide #!48 models
> show #!48 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J303_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J303_003_volume_map_sharp.mrc as #49, grid size 80,80,80,
pixel 3.32, shown at level 0.57, step 1, values float32
> select add #49
2 models selected
> view matrix models
> #49,0.53874,0.84077,0.053573,-61.438,0.83514,-0.54134,0.097405,87.116,0.1109,-0.0077344,-0.9938,260.56
> view matrix models
> #49,0.53215,0.84494,0.053856,-61.154,0.83957,-0.53484,0.095262,85.896,0.10929,-0.0054773,-0.99399,260.49
> view matrix models
> #49,-0.8763,-0.44891,0.17485,296.18,-0.45964,0.88777,-0.024369,82.131,-0.14428,-0.10172,-0.98429,307.41
> volume flip #49
Opened cryosparc_P4_J303_003_volume_map_sharp.mrc z flip as #50, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #49
> rename #50 CS_P4_J303_sharp_flip id #49
> save CS_P4_J303_sharp_flip.mrc #49
> select add #49
2 models selected
> view matrix models
> #49,-0.44927,0.88595,-0.11509,87.376,-0.86051,-0.46376,-0.21085,349.13,-0.24018,0.0043123,0.97072,61.749
> ui mousemode right "translate selected models"
> view matrix models
> #49,-0.44927,0.88595,-0.11509,93.572,-0.86051,-0.46376,-0.21085,352.06,-0.24018,0.0043123,0.97072,37.843
> fitmap #49 inMap 348
Invalid "inMap" argument: invalid density map specifier
> fitmap #49 inMap #48
Fit map CS_P4_J303_sharp_flip.mrc in map CS_P4_J302_sharp_flip.mrc using 5118
points
correlation = 0.8483, correlation about mean = 0.4386, overlap = 3011
steps = 68, shift = 10.7, angle = 7.19 degrees
Position of CS_P4_J303_sharp_flip.mrc (#49) relative to
CS_P4_J302_sharp_flip.mrc (#48) coordinates:
Matrix rotation and translation
0.99996126 -0.00401528 0.00783497 -1.22617333
0.00399514 0.99998870 0.00258400 -1.26181412
-0.00784526 -0.00255260 0.99996598 1.34185977
Axis -0.28004899 0.85489100 0.43673098
Axis point 178.64594040 0.00000000 162.72002408
Rotation angle (degrees) 0.52546068
Shift along axis -0.14929320
> select subtract #49
Nothing selected
> hide #!48 models
> color #49 #FCEDFF
> hide #!49 models
> show #!49 models
> volume #49 level 0.5753
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J304_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J304_002_volume_map_sharp.mrc as #50, grid size 80,80,80,
pixel 3.32, shown at level 1.66, step 1, values float32
> hide #!49 models
> select add #50
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.25626,0.96633,0.023099,-33.544,0.9662,-0.25539,-0.035012,44.222,-0.027934,0.03129,-0.99912,256.23
> volume #50 level 2.579
> select subtract #50
Nothing selected
> volume #50 level 1.975
> volume flip #50
Opened cryosparc_P4_J304_002_volume_map_sharp.mrc z flip as #51, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #50
> rename #51 CS_P4_J304_sharp_flip id #50
> save CS_P4_J304_sharp_flip.mrc #50
> select add #50
2 models selected
> show #!49 models
> view matrix models
> #50,0.25432,0.96619,0.042346,-35.759,0.96711,-0.25431,-0.0057645,40.158,0.0051995,0.042419,-0.99909,250.22
> view matrix models
> #50,-0.77557,0.61543,-0.14049,175.22,-0.61485,-0.78688,-0.052719,333.03,-0.143,0.045495,0.98868,11.993
> color #50 #FCEDFF
> select subtract #50
Nothing selected
> hide #!49 models
> hide #!50 models
> show #!50 models
> volume #50 level 1.954
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J305_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J305_003_volume_map_sharp.mrc as #51, grid size 80,80,80,
pixel 3.32, shown at level 0.569, step 1, values float32
> hide #!50 models
> select add #51
2 models selected
> view matrix models
> #51,-0.9391,-0.22026,0.26379,268.58,-0.1463,0.9508,0.27307,-8.1662,-0.31096,0.21785,-0.92512,264.01
> volume flip #51
Opened cryosparc_P4_J305_003_volume_map_sharp.mrc z flip as #52, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #51
> rename #52 CS_P4_J305_sharp_flip id #51
> save CS_P4_J305_sharp_flip.mrc #51
> color #51 #FCEDFF
> show #!50 models
> select add #51
2 models selected
> view matrix models
> #51,0.99548,-0.078687,0.053201,5.068,0.073705,0.99322,0.089881,-20.578,-0.059913,-0.085553,0.99453,15.159
> fitmap #51 inMap #50
Fit map CS_P4_J305_sharp_flip.mrc in map CS_P4_J304_sharp_flip.mrc using 5112
points
correlation = 0.7769, correlation about mean = 0.3462, overlap = 4325
steps = 92, shift = 6.39, angle = 27.1 degrees
Position of CS_P4_J305_sharp_flip.mrc (#51) relative to
CS_P4_J304_sharp_flip.mrc (#50) coordinates:
Matrix rotation and translation
-0.48191930 -0.86211205 -0.15657780 337.25915719
0.86174903 -0.49867166 0.09335524 70.84333299
-0.15856359 -0.08994107 0.98324371 36.25215794
Axis -0.10573285 0.00114549 0.99439391
Axis point 149.95468753 133.49561797 0.00000000
Rotation angle (degrees) 119.91228641
Shift along axis 0.47070508
> select subtract #51
Nothing selected
> hide #!50 models
> hide #!51 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J306_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J306_002_volume_map_sharp.mrc as #52, grid size 80,80,80,
pixel 3.32, shown at level 0.89, step 1, values float32
> select add #52
2 models selected
> view matrix models
> #52,0.64736,0.71151,-0.27328,-15.881,0.69766,-0.69754,-0.16345,155.65,-0.30692,-0.084848,-0.94795,287.9
> volume flip #52
Opened cryosparc_P4_J306_002_volume_map_sharp.mrc z flip as #53, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #52
> select add #53
2 models selected
> show #!51 models
> view matrix models
> #53,-0.54969,0.82414,-0.13652,114.28,-0.83504,-0.54665,0.062273,314.18,-0.023306,0.14823,0.98868,-59.023
> ui mousemode right "translate selected models"
> view matrix models
> #53,-0.54969,0.82414,-0.13652,112.71,-0.83504,-0.54665,0.062273,313.11,-0.023306,0.14823,0.98868,-22.329
> fitmap #53 inMap #51
Fit map cryosparc_P4_J306_002_volume_map_sharp.mrc z flip in map
CS_P4_J305_sharp_flip.mrc using 5118 points
correlation = 0.8696, correlation about mean = 0.2872, overlap = 4918
steps = 72, shift = 6.47, angle = 20.6 degrees
Position of cryosparc_P4_J306_002_volume_map_sharp.mrc z flip (#53) relative
to CS_P4_J305_sharp_flip.mrc (#51) coordinates:
Matrix rotation and translation
-0.48951817 0.85648171 -0.16374082 109.67271887
-0.85572951 -0.50794021 -0.09860917 331.28158536
-0.16762749 0.09184687 0.98156263 12.77250071
Axis 0.11055185 0.00225605 -0.99386780
Axis point 150.74970822 134.14339059 0.00000000
Rotation angle (degrees) 120.52723515
Shift along axis 0.17773418
> select subtract #53
Nothing selected
> hide #!51 models
> rename #53 CS_P4_J306_sharp_flip id #52
> save CS_P4_J306_sharp_flip.mrc #52
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J307_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J307_002_volume_map_sharp.mrc as #53, grid size 80,80,80,
pixel 3.32, shown at level 0.417, step 1, values float32
> hide #!52 models
> select add #53
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #53,-0.97802,-0.15767,0.13647,275.15,-0.15325,0.98728,0.042392,17.478,-0.14141,0.020547,-0.98974,260.92
> volume flip #53
Opened cryosparc_P4_J307_002_volume_map_sharp.mrc z flip as #54, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #53
> select add #54
2 models selected
> show #!51 models
> view matrix models
> #54,-0.83454,0.54308,0.09272,165.84,-0.53719,-0.83947,0.081916,314.21,0.12232,0.018554,0.99232,-51.868
> ui mousemode right "translate selected models"
> view matrix models
> #54,-0.83454,0.54308,0.09272,166.01,-0.53719,-0.83947,0.081916,312.6,0.12232,0.018554,0.99232,-21.112
> fitmap #54 inMap #51
Fit map cryosparc_P4_J307_002_volume_map_sharp.mrc z flip in map
CS_P4_J305_sharp_flip.mrc using 5118 points
correlation = 0.9157, correlation about mean = 0.3086, overlap = 1346
steps = 92, shift = 8.03, angle = 16.7 degrees
Position of cryosparc_P4_J307_002_volume_map_sharp.mrc z flip (#54) relative
to CS_P4_J305_sharp_flip.mrc (#51) coordinates:
Matrix rotation and translation
-0.49196091 0.85478647 -0.16527113 110.59805296
-0.85414546 -0.51062861 -0.09845785 330.98838770
-0.16855261 0.09272817 0.98132130 13.11747971
Axis 0.11118076 0.00190829 -0.99379837
Axis point 150.81392912 133.83273648 0.00000000
Rotation angle (degrees) 120.70607669
Shift along axis -0.10813355
> select subtract #54
Nothing selected
> rename #54 CS_P4_J307_sharp_flip id #53
> save CS_P4_J307_sharp_flip.mrc #53
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J308_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J308_003_volume_map_sharp.mrc as #54, grid size 80,80,80,
pixel 3.32, shown at level 0.487, step 1, values float32
> hide #!51 models
> hide #!53 models
> select add #54
2 models selected
> view matrix models #54,1,0,0,-2.2085,0,1,0,5.106,0,0,1,17.329
> ui mousemode right "rotate selected models"
> view matrix models
> #54,-0.97907,-0.098429,0.17813,263.99,-0.078474,0.99017,0.11581,3.2524,-0.18778,0.099408,-0.97717,270.12
> volume flip #54
Opened cryosparc_P4_J308_003_volume_map_sharp.mrc z flip as #55, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #54
> select add #55
2 models selected
> show #!53 models
> view matrix models
> #55,-0.032009,-0.99944,0.0094019,279.03,0.99475,-0.030941,0.097574,-4.0943,-0.097229,0.012476,0.99518,-8.8511
> ui mousemode right "translate selected models"
> view matrix models
> #55,-0.032009,-0.99944,0.0094019,275.5,0.99475,-0.030941,0.097574,4.3503,-0.097229,0.012476,0.99518,10.879
> fitmap #55 inMap #53
Fit map cryosparc_P4_J308_003_volume_map_sharp.mrc z flip in map
CS_P4_J307_sharp_flip.mrc using 5116 points
correlation = 0.9635, correlation about mean = 0.3444, overlap = 1309
steps = 80, shift = 11, angle = 8.02 degrees
Position of cryosparc_P4_J308_003_volume_map_sharp.mrc z flip (#55) relative
to CS_P4_J307_sharp_flip.mrc (#53) coordinates:
Matrix rotation and translation
-0.47079667 0.87008681 -0.14594324 102.09450866
-0.87101131 -0.48471046 -0.07996914 326.37268834
-0.14032031 0.08946901 0.98605553 9.07494900
Axis 0.09685875 -0.00321433 -0.99529295
Axis point 148.07793015 132.95152312 0.00000000
Rotation angle (degrees) 118.99450917
Shift along axis -0.19255539
> select subtract #55
Nothing selected
> hide #!53 models
> color #55 #fcedffff models
> rename #55 CS_P4_J308_sharp_flip id #54
> save CS_P4_J308_sharp_flip.mrc #54
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J309_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J309_002_volume_map_sharp.mrc as #55, grid size 80,80,80,
pixel 3.32, shown at level 0.427, step 1, values float32
> hide #!54 models
> select add #55
2 models selected
> show #!54 models
> ui mousemode right "rotate selected models"
> view matrix models
> #55,0.72482,-0.68817,-0.032661,133.9,-0.68882,-0.72298,-0.053201,331.74,0.012998,0.061058,-0.99805,234.36
> hide #!54 models
> view matrix models
> #55,-0.98503,0.14104,0.099091,242.98,0.14443,0.98912,0.027904,-21.89,-0.094078,0.041798,-0.99469,251.29
> volume flip #55
Opened cryosparc_P4_J309_002_volume_map_sharp.mrc z flip as #56, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #55
> select add #56
2 models selected
> show #!54 models
> view matrix models
> #56,-0.63923,0.76709,0.054278,117.91,-0.76391,-0.64153,0.069883,315.42,0.088428,0.0032076,0.99608,-48.086
> ui mousemode right "translate selected models"
> view matrix models
> #56,-0.63923,0.76709,0.054278,118.17,-0.76391,-0.64153,0.069883,313.6,0.088428,0.0032076,0.99608,-18.356
> fitmap #56 inMap #54
Fit map cryosparc_P4_J309_002_volume_map_sharp.mrc z flip in map
CS_P4_J308_sharp_flip.mrc using 5111 points
correlation = 0.9585, correlation about mean = 0.3571, overlap = 1283
steps = 104, shift = 10.8, angle = 17.1 degrees
Position of cryosparc_P4_J309_002_volume_map_sharp.mrc z flip (#56) relative
to CS_P4_J308_sharp_flip.mrc (#54) coordinates:
Matrix rotation and translation
-0.48831434 -0.86312376 -0.12871093 333.56502617
0.86459679 -0.49852007 0.06285020 75.43057430
-0.11841248 -0.08059241 0.98968852 28.18171624
Axis -0.08273806 -0.00594017 0.99655362
Axis point 146.06051902 134.60897835 0.00000000
Rotation angle (degrees) 119.90563147
Shift along axis 0.03799683
> select subtract #56
Nothing selected
> hide #!54 models
> hide #!56 models
> show #!56 models
> color #56 #fcedffff models
> rename #56 CS_P4_J309_sharp_flip id #55
> save CS_P4_J309_sharp_flip.mrc #55
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J310_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J310_003_volume_map_sharp.mrc as #56, grid size 80,80,80,
pixel 3.32, shown at level 0.683, step 1, values float32
> volume flip #56
Opened cryosparc_P4_J310_003_volume_map_sharp.mrc z flip as #57, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #56
> fitmap #56 inMap #52
No atoms or maps for #56
> fitmap #57 inMap #52
Fit map cryosparc_P4_J310_003_volume_map_sharp.mrc z flip in map
CS_P4_J306_sharp_flip.mrc using 5115 points
correlation = 0.769, correlation about mean = 0.3701, overlap = 4288
steps = 88, shift = 5.42, angle = 22.7 degrees
Position of cryosparc_P4_J310_003_volume_map_sharp.mrc z flip (#57) relative
to CS_P4_J306_sharp_flip.mrc (#52) coordinates:
Matrix rotation and translation
-0.48166864 -0.85899522 -0.17355843 339.66736714
0.86194402 -0.50013127 0.08319372 72.72621082
-0.15826501 -0.10952585 0.98130335 38.95738038
Axis -0.11128512 -0.00883113 0.99374928
Axis point 150.89500052 135.18260516 0.00000000
Rotation angle (degrees) 120.01642768
Shift along axis 0.27169032
> hide #!55 models
> show #!52 models
> color #57 #fcedffff models
> hide #!52 models
> save #57 CS_P4_J310_sharp_flip id #56
Cannot determine format for '#57'
> rename #57 CS_P4_J310_sharp_flip id #56
> save CS_P4_J310_sharp_flip.mrc #56
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J311_004_volume_map_sharp.mrc"
Opened cryosparc_P4_J311_004_volume_map_sharp.mrc as #57, grid size 80,80,80,
pixel 3.32, shown at level 0.525, step 1, values float32
> volume flip #57
Opened cryosparc_P4_J311_004_volume_map_sharp.mrc z flip as #58, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #57
> color #58 #fcedffff models
> rename #58 CS_P4_J311_sharp_flip id #57
> save CS_P4_J311_sharp_flip.mrc #57
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260506_SA-F_B1_workflow.cxs"
> view P1
> hide #!57 models
> hide #!56 models
> show #!47 models
> hide #!47 models
> show #!48 models
> save CS_P4_J302_NU_sharp.png supersample 3 transparentBackground true
> hide #!48 models
> show #!49 models
> save CS_P4_J303_NU_sharp.png supersample 3 transparentBackground true
> hide #!49 models
> show #!50 models
> save CS_P4_J304_NU_sharp.png supersample 3 transparentBackground true
> hide #!50 models
> show #!51 models
> save CS_P4_J305_NU_sharp.png supersample 3 transparentBackground true
> hide #!51 models
> show #!52 models
> volume #52 level 1.034
> save CS_P4_J306_NU_sharp.png supersample 3 transparentBackground true
> hide #!52 models
> show #!53 models
> color #53 #fcedffff models
> save CS_P4_J307_NU_sharp.png supersample 3 transparentBackground true
> hide #!53 models
> show #!54 models
> save CS_P4_J308_NU_sharp.png supersample 3 transparentBackground true
> hide #!54 models
> show #!55 models
> save CS_P4_J309_NU_sharp.png supersample 3 transparentBackground true
> hide #!55 models
> show #!56 models
> volume #56 level 0.7192
> save CS_P4_J310_NU_sharp.png supersample 3 transparentBackground true
> hide #!56 models
> show #!57 models
> save CS_P4_J311_NU_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260506_SA-F_B1_workflow.cxs"
——— End of log from Wed May 6 15:19:28 2026 ———
> view name session-start
opened ChimeraX session
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J323_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J323_006_volume_map_sharp.mrc as #58, grid size
320,320,320, pixel 0.831, shown at level 0.0345, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J324_map_locres.mrc"
Opened cryosparc_P4_J324_map_locres.mrc as #59, grid size 320,320,320, pixel
0.831, shown at level 8.89, step 2, values float32
> hide #!57 models
> hide #!58 models
> show #!58 models
> hide #!59 models
> show #!59 models
> volume flip #58
Opened cryosparc_P4_J323_006_volume_map_sharp.mrc z flip as #60, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #59
Opened cryosparc_P4_J324_map_locres.mrc z flip as #61, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> close #58
> close #59
> rename #60 CS_P4_J323_sharp_flip #58
Expected a keyword
> rename #60 CS_P4_J323_sharp_flip id #58
> save CS_P4_J323_sharp_flip.mrc #58
> rename CS_P4_J324_map_locres_flip id #59
Missing or invalid "models" argument: invalid models specifier
> rename #61 CS_P4_J324_map_locres_flip id #59
> save CS_P4_J324_map_locres_flip.mrc #59
> hide #!58 models
> show #!58 models
> hide #!59 models
> volume #59 level 9.377
> hide #!59 models
> volume #58 level 0.05889
> show #!59 models
> volume #59 level 3.695
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow.cxs"
> ui tool show "Surface Color"
> hide #!58 models
> show #!58 models
> hide #!59 models
> color radial #58.1 palette #ffb17f:#4979d3:#99bfe5:#fff6c0:#f4fff3
> color sample #58.1 map #59 palette
> 166.9,#ffb17f:198,#4979d3:229.1,#99bfe5:260.3,#fff6c0:291.4,#f4fff3
> outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.552, maximum 44.59
> color sample #58.1 map #59 palette
> 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.552, maximum 44.59
> show #!59 models
> hide #!58 models
> hide #!59 models
> show #!59 models
> show #!58 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> volume #58 level 0.0634
> volume #58 level 0.04264
> volume #58 level 0.07693
> volume #58 level 0.06069
> volume #58 level 0.07152
> volume #58 level 0.05889
> volume #58 level 0.05167
> volume #58 level 0.06159
> key #ffb17f:2 #4979d3:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> key pos 0.82265,0.196044 size 0.0692066,0.202924
> ui mousemode right translate
> ui mousemode right "color key"
> key pos 0.802943,0.231339 size 0.039822,0.144632
> key #ffb17f:2 #4979d3:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> key pos 0.836801,0.165731 size 0.0516869,0.238605
> show #41 models
> key pos 0.820538,0.190547 size 0.0458442,0.242723
> save CS_P4_J323_sharp_flip.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow1.cxs"
> color sample #58.1 map #59 palette
> 2,#ffb17f:3,#169bd3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> color sample #58.1 map #59 palette
> 2,#ffb17f:3,#46c7f6:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> color sample #58.1 map #59 palette
> 2,#ffb17f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> key #ffb17f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> color sample #58.1 map #59 palette
> 2,#ffb17f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> key #ffb17f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true
> color sample #58.1 map #59 palette
> 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> key #13097f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true
> save CS_P4_J323_sharp_flip2.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow2.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J329_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J329_005_volume_map_sharp.mrc as #60, grid size
320,320,320, pixel 0.831, shown at level 0.0384, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J330_map_locres.mrc"
Opened cryosparc_P4_J330_map_locres.mrc as #61, grid size 320,320,320, pixel
0.831, shown at level 9.71, step 2, values float32
> hide #!58 models
> hide #!60 models
> show #!60 models
> hide #!61 models
> volume flip #60
Opened cryosparc_P4_J329_005_volume_map_sharp.mrc z flip as #62, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #61
Opened cryosparc_P4_J330_map_locres.mrc z flip as #63, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> close #60
> close #61
> rename #62 CS_P4_J329_sharp_flip id #60
> save CS_P4_J329_sharp_flip.mrc #60
> rename #63 rename
> rename #63 CS_P4_J330_locres_flip id #61
> save CS_P4_J330_locres_flip.mrc #61
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow3.cxs"
> hide #!61 models
> color sample #58.1 map #59 palette
> 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> color sample #60.1 map #61 palette
> 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.466, maximum 46.71
> volume #60 level 0.06443
> key #13097f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true
> ui mousemode right "color key"
> volume #60 level 0.05663
> save CS_P4_J329_locres_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow3.cxs"
——— End of log from Thu May 7 15:58:17 2026 ———
> view name session-start
opened ChimeraX session
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J300_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J300_005_volume_map_sharp.mrc as #62, grid size
320,320,320, pixel 0.831, shown at level 0.0375, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J301_map_locres.mrc"
Opened cryosparc_P4_J301_map_locres.mrc as #63, grid size 320,320,320, pixel
0.831, shown at level 9.68, step 2, values float32
> hide #!60 models
> hide #!63 models
> volume flip #62
Opened cryosparc_P4_J300_005_volume_map_sharp.mrc z flip as #64, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #63
Opened cryosparc_P4_J301_map_locres.mrc z flip as #65, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> close #62
> close #63
> rename #64 CS_P4_J300_sharp_flip id #62
> save CS_P4_J300_sharp_flip.mrc #62
> rename #65 CS_P4_J301_locres_flip id #63
> save CS_P4_J301_locres_flip.mrc #63
> show #!46 models
> show #!47 models
> hide #!47 models
> hide #!46 models
> hide #!63 models
> show #!63 models
> volume #63 level 3.952
> hide #!63 models
> volume #62 level 0.0392
> ui tool show "Surface Color"
> color sample #62.1 map #63 palette #13097f:#11b6e1:#99bfe5:#fff6c0:#ffb17f
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.383, maximum 43.37
> color sample #62.1 map #63 palette
> 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.383, maximum 43.37
> show #!63 models
> hide #!63 models
> hide #!62 models
> show #!62 models
> volume #62 level 0.06614
> volume #62 level 0.05745
> save CS_P4_J300_locres_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow4.cxs"
> open /Users/peiyuyu/Downloads/cryosparc_P7_J110_004_volume_map_sharp.mrc
Opened cryosparc_P7_J110_004_volume_map_sharp.mrc as #64, grid size
160,160,160, pixel 1.66, shown at level 0.28, step 1, values float32
> hide #!62 models
> close #64
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow5.cxs"
——— End of log from Thu May 7 21:11:39 2026 ———
> view name session-start
opened ChimeraX session
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J323_006_volume_map_sharp2.mrc"
Opened cryosparc_P4_J323_006_volume_map_sharp2.mrc as #64, grid size
320,320,320, pixel 0.831, shown at level 0.0329, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J324_map_locres2.mrc"
Opened cryosparc_P4_J324_map_locres2.mrc as #65, grid size 320,320,320, pixel
0.831, shown at level 8.98, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J329_006_volume_map_sharp2.mrc"
Opened cryosparc_P4_J329_006_volume_map_sharp2.mrc as #66, grid size
320,320,320, pixel 0.831, shown at level 0.0389, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J330_map_locres2.mrc"
Opened cryosparc_P4_J330_map_locres2.mrc as #67, grid size 320,320,320, pixel
0.831, shown at level 9.65, step 2, values float32
> hide #!66 models
> hide #!67 models
> hide #!65 models
> close #66
> close #67
> volume flip #64
Opened cryosparc_P4_J323_006_volume_map_sharp2.mrc z flip as #66, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #65
Opened cryosparc_P4_J324_map_locres2.mrc z flip as #67, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> volume #66 level 0.04422
> volume #67 level 3.812
> hide #!66 models
> hide #!67 models
> show #!67 models
> hide #!67 models
> show #!66 models
> close #64
> close #65
> rename #66 CS_P4_J323_sharp2_flip id #64
> save CS_P4_J323_sharp2_flip.mrc #64
> rename CS_P4_J324_locres2_flip id #65
Missing or invalid "models" argument: invalid models specifier
> rename CS_P4_J324_locres2_flip id #65
Missing or invalid "models" argument: invalid models specifier
> rename #67 CS_P4_J324_locres2_flip id #65
> save CS_P4_J324_locres2_flip.mrc #65
> hide #!64 models
> show #!65 models
> hide #!65 models
> show #!64 models
> volume #64 level 0.05469
> ui tool show "Surface Color"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow5.cxs"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel
2.08, shown at level 0.185, step 1, values float32
Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel
2.08, shown at level 0.203, step 1, values float32
Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel
2.08, shown at level 0.356, step 1, values float32
Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown
at level 1.17, step 1, values float32
Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel
2.08, shown at level 0.335, step 1, values float32
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown
at level 1.29, step 1, values float32
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel
2.08, shown at level 0.271, step 1, values float32
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32
Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32,
shown at level 1.6, step 1, values float32
Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown
at level 0.649, step 1, values float32
Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown
at level 1.01, step 1, values float32
Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown
at level 0.533, step 1, values float32
Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown
at level 0.567, step 1, values float32
Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831,
shown at level 0.134, step 1, values float32
Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831,
shown at level 0.143, step 1, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 3.78, step 2, values float32
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 3.77, step 2, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at level 3.78, step 1, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at level 3.77, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0602, step 2, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32
Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831,
shown at level 0.0515, step 1, values float32
Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831,
shown at level 8.66, step 1, values float32
Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831,
shown at level 0.0592, step 1, values float32
Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831,
shown at level 9.68, step 1, values float32
Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown
at level 0.612, step 1, values float32
Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown
at level 0.575, step 1, values float32
Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown
at level 1.95, step 1, values float32
Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown
at level 0.569, step 1, values float32
Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown
at level 1.03, step 1, values float32
Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown
at level 0.417, step 1, values float32
Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown
at level 0.487, step 1, values float32
Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown
at level 0.427, step 1, values float32
Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown
at level 0.719, step 1, values float32
Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown
at level 0.525, step 1, values float32
Opened CS_P4_J323_sharp_flip.mrc as #58, grid size 320,320,320, pixel 0.831,
shown at level 0.0616, step 1, values float32
Opened CS_P4_J324_map_locres_flip.mrc as #59, grid size 320,320,320, pixel
0.831, shown at level 3.69, step 1, values float32
Opened CS_P4_J329_sharp_flip.mrc as #60, grid size 320,320,320, pixel 0.831,
shown at level 0.0566, step 1, values float32
Opened CS_P4_J330_locres_flip.mrc as #61, grid size 320,320,320, pixel 0.831,
shown at level 9.71, step 1, values float32
Opened CS_P4_J300_sharp_flip.mrc as #62, grid size 320,320,320, pixel 0.831,
shown at level 0.0575, step 1, values float32
Opened CS_P4_J301_locres_flip.mrc as #63, grid size 320,320,320, pixel 0.831,
shown at level 3.95, step 1, values float32
Log from Thu May 7 21:11:39 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow3.cxs"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel
2.08, shown at level 0.185, step 1, values float32
Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel
2.08, shown at level 0.203, step 1, values float32
Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel
2.08, shown at level 0.356, step 1, values float32
Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown
at level 1.17, step 1, values float32
Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel
2.08, shown at level 0.335, step 1, values float32
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown
at level 1.29, step 1, values float32
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel
2.08, shown at level 0.271, step 1, values float32
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32
Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32,
shown at level 1.6, step 1, values float32
Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown
at level 0.649, step 1, values float32
Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown
at level 1.01, step 1, values float32
Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown
at level 0.533, step 1, values float32
Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown
at level 0.567, step 1, values float32
Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831,
shown at level 0.134, step 1, values float32
Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831,
shown at level 0.143, step 1, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 3.78, step 2, values float32
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 3.77, step 2, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at level 3.78, step 1, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at level 3.77, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0602, step 2, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32
Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831,
shown at level 0.0515, step 1, values float32
Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831,
shown at level 8.66, step 1, values float32
Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831,
shown at level 0.0592, step 1, values float32
Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831,
shown at level 9.68, step 1, values float32
Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown
at level 0.612, step 1, values float32
Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown
at level 0.575, step 1, values float32
Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown
at level 1.95, step 1, values float32
Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown
at level 0.569, step 1, values float32
Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown
at level 1.03, step 1, values float32
Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown
at level 0.417, step 1, values float32
Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown
at level 0.487, step 1, values float32
Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown
at level 0.427, step 1, values float32
Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown
at level 0.719, step 1, values float32
Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown
at level 0.525, step 1, values float32
Opened CS_P4_J323_sharp_flip.mrc as #58, grid size 320,320,320, pixel 0.831,
shown at level 0.0616, step 1, values float32
Opened CS_P4_J324_map_locres_flip.mrc as #59, grid size 320,320,320, pixel
0.831, shown at level 3.69, step 1, values float32
Opened CS_P4_J329_sharp_flip.mrc as #60, grid size 320,320,320, pixel 0.831,
shown at level 0.0566, step 1, values float32
Opened CS_P4_J330_locres_flip.mrc as #61, grid size 320,320,320, pixel 0.831,
shown at level 9.71, step 1, values float32
Log from Thu May 7 15:58:17 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260506_SA-F_B1_workflow.cxs"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel
2.08, shown at level 0.185, step 1, values float32
Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel
2.08, shown at level 0.203, step 1, values float32
Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel
2.08, shown at level 0.356, step 1, values float32
Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown
at level 1.17, step 1, values float32
Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel
2.08, shown at level 0.335, step 1, values float32
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown
at level 1.29, step 1, values float32
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel
2.08, shown at level 0.271, step 1, values float32
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32
Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32,
shown at level 1.6, step 1, values float32
Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown
at level 0.649, step 1, values float32
Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown
at level 1.01, step 1, values float32
Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown
at level 0.533, step 1, values float32
Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown
at level 0.567, step 1, values float32
Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831,
shown at level 0.134, step 1, values float32
Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831,
shown at level 0.143, step 1, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 3.78, step 2, values float32
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 3.77, step 2, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at level 3.78, step 1, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at level 3.77, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0602, step 2, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32
Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831,
shown at level 0.0515, step 1, values float32
Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831,
shown at level 8.66, step 1, values float32
Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831,
shown at level 0.0592, step 1, values float32
Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831,
shown at level 9.68, step 1, values float32
Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown
at level 0.612, step 1, values float32
Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown
at level 0.575, step 1, values float32
Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown
at level 1.95, step 1, values float32
Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown
at level 0.569, step 1, values float32
Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown
at level 1.03, step 1, values float32
Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown
at level 0.417, step 1, values float32
Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown
at level 0.487, step 1, values float32
Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown
at level 0.427, step 1, values float32
Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown
at level 0.719, step 1, values float32
Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown
at level 0.525, step 1, values float32
Log from Wed May 6 15:19:28 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260505_SA-F_B1_workflow.cxs"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel
2.08, shown at level 0.185, step 1, values float32
Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel
2.08, shown at level 0.203, step 1, values float32
Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel
2.08, shown at level 0.356, step 1, values float32
Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown
at level 1.17, step 1, values float32
Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel
2.08, shown at level 0.335, step 1, values float32
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown
at level 1.29, step 1, values float32
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel
2.08, shown at level 0.271, step 1, values float32
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32
Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32,
shown at level 1.6, step 1, values float32
Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown
at level 0.649, step 1, values float32
Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown
at level 1.01, step 1, values float32
Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown
at level 0.533, step 1, values float32
Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown
at level 0.567, step 1, values float32
Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831,
shown at level 0.134, step 1, values float32
Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831,
shown at level 0.143, step 1, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 3.78, step 2, values float32
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 3.77, step 2, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at level 3.78, step 1, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at level 3.77, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0602, step 2, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32
Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831,
shown at level 0.0515, step 1, values float32
Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831,
shown at level 8.66, step 1, values float32
Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831,
shown at level 0.0592, step 1, values float32
Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831,
shown at level 9.68, step 1, values float32
Log from Tue May 5 09:31:57 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow4.cxs"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel
2.08, shown at level 0.185, step 1, values float32
Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel
2.08, shown at level 0.203, step 1, values float32
Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel
2.08, shown at level 0.356, step 1, values float32
Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown
at level 1.17, step 1, values float32
Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel
2.08, shown at level 0.335, step 1, values float32
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown
at level 1.29, step 1, values float32
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel
2.08, shown at level 0.271, step 1, values float32
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32
Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32,
shown at level 1.6, step 1, values float32
Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown
at level 0.649, step 1, values float32
Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown
at level 1.01, step 1, values float32
Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown
at level 1.16, step 1, values float32
Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown
at level 0.533, step 1, values float32
Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown
at level 0.567, step 1, values float32
Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831,
shown at level 0.134, step 1, values float32
Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831,
shown at level 0.143, step 1, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 3.78, step 2, values float32
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 3.77, step 2, values float32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at level 3.78, step 1, values float32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at level 3.77, step 1, values float32
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0602, step 2, values float32
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32
Log from Sun May 3 17:29:06 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J216_class_00_00122_volume_sharp.mrc"
Opened cryosparc_P4_J216_class_00_00122_volume_sharp.mrc as #1, grid size
128,128,128, pixel 2.08, shown at level 0.204, step 1, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J216_class_01_00122_volume_sharp.mrc"
Opened cryosparc_P4_J216_class_01_00122_volume_sharp.mrc as #2, grid size
128,128,128, pixel 2.08, shown at level 0.218, step 1, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J216_class_02_00122_volume_sharp.mrc"
Opened cryosparc_P4_J216_class_02_00122_volume_sharp.mrc as #3, grid size
128,128,128, pixel 2.08, shown at level 0.263, step 1, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J216_class_03_00122_volume_sharp.mrc"
Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.08, shown at level 0.199, step 1, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J216_class_04_00122_volume_sharp.mrc"
Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.08, shown at level 0.235, step 1, values float32
> lighting soft
> set bgColor white
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!4 models
> volume #4 level 0.2842
> show #!3 models
> hide #!4 models
> volume #3 level 0.3546
> volume #3 level 0.356
> hide #!3 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!1 models
> color #1 #FCEDFF
> hide #!5 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!1 models
> volume flip #1
Opened cryosparc_P4_J216_class_00_00122_volume_sharp.mrc z flip as #6, grid
size 128,128,128, pixel 2.08, shown at step 1, values float32
> hide #!6 models
> show #!2 models
> volume flip #2
Opened cryosparc_P4_J216_class_01_00122_volume_sharp.mrc z flip as #7, grid
size 128,128,128, pixel 2.08, shown at step 1, values float32
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> volume flip #3
Opened cryosparc_P4_J216_class_02_00122_volume_sharp.mrc z flip as #8, grid
size 128,128,128, pixel 2.08, shown at step 1, values float32
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!8 models
> hide #!5 models
> close #1
> close #2
> close #3
> rename #6 CS_P4_J216_class_0_sharp_flip id #1
> save #1 CS_P4_J216_class_0_sharp_flip.mrc
Cannot determine format for '#1'
> save CS_P4_J216_class_0_sharp_flip.mrc #1
> rename #7 CS_P4_J216_class_1_sharp_flip id #1_sharp_flip.mrc #2
Invalid "id" argument: Expected an integer
> rename #7 CS_P4_J216_class_1_sharp_flip id #1_sharp_flip id #2
Invalid "id" argument: Expected an integer
> rename #7 CS_P4_J216_class_2_sharp_flip id #2
> rename #2 CS_P4_J216_class_1_sharp_flip
> rename #8 CS_P4_J216_class_2_sharp_flip id #3
> save CS_P4_J216_class_1_sharp_flip.mrc #2
> save CS_P4_J216_class_2_sharp_flip.mrc #3
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260430_SA-F_B1_workflow.cxs"
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!5 models
> show #!3 models
> hide #!5 models
> show #!1 models
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-2.4868,0,1,0,6.8233,0,0,1,22.302
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.85834,-0.51214,-0.03115,83.967,-0.50924,-0.85776,0.070198,298.29,-0.06267,-0.044391,-0.99705,270.86
Must specify one map, got 0
> fitmap #1 inMap #3
Fit map CS_P4_J216_class_0_sharp_flip.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 20952 points
correlation = 0.8163, correlation about mean = 0.111, overlap = 1135
steps = 116, shift = 13.1, angle = 14.8 degrees
Position of CS_P4_J216_class_0_sharp_flip.mrc (#1) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.94377261 -0.32509802 0.06003771 31.40521096
-0.32212557 -0.94514622 -0.05416389 308.66342237
0.07435299 0.03177871 -0.99672551 251.62777867
Axis 0.98583616 -0.16420866 0.03409658
Axis point 0.00000000 154.16030965 128.66405805
Rotation angle (degrees) 177.50176084
Shift along axis -11.14516800
> select subtract #1
Nothing selected
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!3 models
> fitmap #2 inMap #3
Fit map CS_P4_J216_class_1_sharp_flip.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 20964 points
correlation = 0.8775, correlation about mean = 0.2387, overlap = 1535
steps = 72, shift = 7.04, angle = 9.35 degrees
Position of CS_P4_J216_class_1_sharp_flip.mrc (#2) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.99017956 0.04949629 -0.13074615 12.42570756
-0.06022022 0.99502365 -0.07938169 18.18421737
0.12616642 0.08647569 0.98823276 -19.36289944
Axis 0.51051058 -0.79077932 -0.33770846
Axis point 165.72686650 0.00000000 88.43510724
Rotation angle (degrees) 9.34870453
Shift along axis -1.49723285
> hide #!2 models
> show #!4 models
> fitmap #4 inMap #3
Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 5887 points
correlation = 0.7186, correlation about mean = 0.04573, overlap = 331.9
steps = 104, shift = 11.1, angle = 13.1 degrees
Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.97455290 -0.13512397 0.17885231 -1.53434267
0.14053006 0.98991548 -0.01785084 -17.74958210
-0.17463660 0.04253071 0.98371398 30.92421506
Axis 0.13349556 0.78151692 0.60943437
Axis point 157.21397711 0.00000000 34.50744362
Rotation angle (degrees) 13.07084305
Shift along axis 4.76985279
> hide #!4 models
> show #!5 models
> select add #5
2 models selected
> view matrix models
> #5,0.70232,-0.70945,-0.058532,142.48,-0.70661,-0.70474,0.063551,312.49,-0.086337,-0.0032735,-0.99626,292.78
> fitmap #5 inMap #3
Fit map cryosparc_P4_J216_class_04_00122_volume_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 20952 points
correlation = 0.896, correlation about mean = 0.3255, overlap = 1903
steps = 100, shift = 4.43, angle = 13 degrees
Position of cryosparc_P4_J216_class_04_00122_volume_sharp.mrc (#5) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.72688934 -0.68457986 0.05461051 119.19907428
-0.67457364 -0.72664609 -0.13013783 337.91149541
0.12877226 0.05775699 -0.98999082 252.38058253
Axis 0.92902840 -0.36668580 0.04947481
Axis point 0.00000000 185.59312596 132.22855036
Rotation angle (degrees) 174.19607958
Shift along axis -0.68154259
> select subtract #5
Nothing selected
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260430_SA-F_B1_workflow.cxs"
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!2 models
> color #2 #FCEDFF
> hide #!2 models
> show #!4 models
> color #4 #FCEDFF
> hide #!4 models
> show #!5 models
> color #5 #FCEDFF
> hide #!5 models
> show #!3 models
> color #5 #E9C29B
> color #5 #FCEDFF
> color #3 #E9C29B
> ui mousemode right translate
> volume #2 level 0.356
> volume #1 level 0.356
> volume #4 level 0.356
> volume #5 level 0.356
> hide #!3 models
> show #!1 models
> undo
[Repeated 1 time(s)]
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.1727
> volume #1 level 0.1851
> show #!2 models
> hide #!1 models
> volume #2 level 0.203
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!4 models
> volume #4 level 0.1532
> show #!3 models
> select add #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.97455,-0.13512,0.17885,1.3208,0.14053,0.98992,-0.017851,-10.868,-0.17464,0.042531,0.98371,31.337
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.085498,-0.64922,0.75578,120.23,0.99605,-0.074063,0.049058,8.8958,0.024125,0.75698,0.65299,-39.323
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.085498,-0.64922,0.75578,134.23,0.99605,-0.074063,0.049058,6.1939,0.024125,0.75698,0.65299,-87.477
> view matrix models
> #4,-0.085498,-0.64922,0.75578,134.33,0.99605,-0.074063,0.049058,6.22,0.024125,0.75698,0.65299,-87.742
> view matrix models
> #4,-0.085498,-0.64922,0.75578,130.4,0.99605,-0.074063,0.049058,5.0583,0.024125,0.75698,0.65299,-76.883
> fitmap #4 inMap #3
Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 42435 points
correlation = 0.7796, correlation about mean = 0.1614, overlap = 1558
steps = 228, shift = 2.07, angle = 23.4 degrees
Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.31733316 -0.35582789 0.87902570 104.58434579
0.93180439 -0.28920783 0.21931579 18.83015631
0.17618244 0.88867618 0.42333722 -81.48445272
Axis 0.41511738 0.43588247 0.79855121
Axis point 65.64014873 66.59534740 0.00000000
Rotation angle (degrees) 126.27076538
Shift along axis -13.44699307
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.85396,0.083596,-0.51358,313.46,-0.52034,-0.13698,0.8429,94.578,0.00011363,0.98704,0.16047,-34.579
> fitmap #4 inMap #3
Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 42435 points
correlation = 0.7628, correlation about mean = 0.1138, overlap = 1507
steps = 160, shift = 8.1, angle = 11.6 degrees
Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.75756109 0.20637267 -0.61928307 295.50473254
-0.63935005 -0.04324082 0.76769900 115.47474727
0.13165378 0.97751755 0.16470194 -51.62941296
Axis 0.18240424 -0.65282152 -0.73522293
Axis point 168.50534676 17.73009752 0.00000000
Rotation angle (degrees) 144.89006320
Shift along axis 16.47604383
> select subtract #4
Nothing selected
> volume #4 level 0.3211
> hide #!3 models
> volume #4 level 0.2347
> volume #4 level 0.2031
> hide #!4 models
> show #!5 models
> volume #5 level 0.1924
> volume #5 level 0.2064
> ui mousemode right translate
> show #!3 models
> hide #!5 models
> color #3 #B9DBD5
> hide #!3 models
> show #!1 models
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> save P4_J216_class_0_sharp.png supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save P4_J216_class_1_sharp.png supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> save P4_J216_class_2_sharp.png supersample 3 transparentBackground true
> hide #!3 models
> show #!4 models
> save P4_J216_class_3_sharp.png supersample 3 transparentBackground true
> hide #!4 models
> show #!5 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> view name P1
[Repeated 1 time(s)]
> save P4_J216_class_0_sharp.png supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save P4_J216_class_1_sharp.png supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> save P4_J216_class_2_sharp.png supersample 3 transparentBackground true
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> save P4_J216_class_3_sharp.png supersample 3 transparentBackground true
> hide #!4 models
> show #!5 models
> vieww P1
Unknown command: vieww P1
> view P1
[Repeated 1 time(s)]
> save P4_J216_class_4_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260430_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J219_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J219_002_volume_map_sharp.mrc as #6, grid size 80,80,80,
pixel 3.32, shown at level 0.854, step 1, values float32
> hide #!5 models
> show #!3 models
> select add #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.50968,-0.8597,0.033732,182.49,-0.85693,-0.50376,0.10903,313.05,-0.076743,-0.084479,-0.99347,263.76
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.50968,-0.8597,0.033732,181.37,-0.85693,-0.50376,0.10903,307.2,-0.076743,-0.084479,-0.99347,286.3
> fitmap #6 inMap #3
Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 5120 points
correlation = 0.7368, correlation about mean = 0.07448, overlap = 1741
steps = 88, shift = 8.42, angle = 12.4 degrees
Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.68179907 -0.73031354 0.04233404 134.55628275
-0.72995927 -0.67538450 0.10495351 308.10402853
-0.04805721 -0.10245933 -0.99357566 283.32032359
Axis -0.91672636 0.39951261 0.00156579
Axis point 0.00000000 192.14085888 132.24148806
Rotation angle (degrees) 173.50439997
Shift along axis 0.18377410
> volume #6 level 1.828
> select subtract #6
Nothing selected
> hide #!3 models
> volume #6 level 1.172
> show #!3 models
> select add #6
2 models selected
> view matrix models
> #6,0.6818,-0.73031,0.042334,145.51,-0.72996,-0.67538,0.10495,294.75,-0.048057,-0.10246,-0.99358,285.84
> view matrix models
> #6,0.6818,-0.73031,0.042334,133.79,-0.72996,-0.67538,0.10495,309.04,-0.048057,-0.10246,-0.99358,282.76
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.47143,0.87224,0.13024,-67.58,0.87592,-0.44591,-0.18423,88.863,-0.10262,0.20093,-0.97422,246.36
> fitmap #6 inMap #3
Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 3507 points
correlation = 0.7523, correlation about mean = 0.053, overlap = 1436
steps = 84, shift = 11, angle = 9.96 degrees
Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
0.31271016 0.94213099 0.12083688 -48.05138587
0.94223385 -0.29160641 -0.16480619 65.68302492
-0.12003221 0.16539317 -0.97889599 255.74245569
Axis 0.80789250 0.58932983 0.00025166
Axis point 0.00000000 34.02227920 132.07845223
Rotation angle (degrees) 168.20805262
Shift along axis -0.04702893
> select subtract #6
Nothing selected
> hide #!6 models
> show #!6 models
> select add #6
2 models selected
> view matrix models
> #6,-0.96774,-0.18791,0.16785,278.55,-0.18769,0.98208,0.017294,25.636,-0.16809,-0.014768,-0.98566,287.91
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.96774,-0.18791,0.16785,272.6,-0.18769,0.98208,0.017294,32.876,-0.16809,-0.014768,-0.98566,284.26
> fitmap #6 inMap #3
Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 3507 points
correlation = 0.7248, correlation about mean = 0.05418, overlap = 1264
steps = 60, shift = 9.72, angle = 10.6 degrees
Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.92647017 -0.30027989 0.22690311 266.55888821
-0.26721766 0.94935570 0.16528304 28.41095713
-0.26504293 0.09249729 -0.95978982 282.00607809
Axis -0.14603906 0.98705219 0.06633684
Axis point 153.43261550 0.00000000 122.88099835
Rotation angle (degrees) 165.56984584
Shift along axis 7.82248126
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.92785,-0.005043,0.37292,209.61,0.027742,0.99621,0.082497,-9.3167,-0.37192,0.086891,-0.92419,293.48
> fitmap #6 inMap #3
Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 3507 points
correlation = 0.7519, correlation about mean = 0.05711, overlap = 1436
steps = 100, shift = 5.47, angle = 14.5 degrees
Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.92643320 -0.21423055 0.30955905 249.03084383
-0.21368345 0.97623560 0.03610312 27.35482068
-0.30993696 -0.03270052 -0.95019459 303.95121642
Axis -0.11038513 0.99388850 0.00087774
Axis point 150.47041621 0.00000000 131.94319456
Rotation angle (degrees) 161.84114382
Shift along axis -0.03486954
> select subtract #6
Nothing selected
> hide #!3 models
> hide #!6 models
> show #!3 models
> hide #!3 models
> show #!6 models
> volume flip #6
Opened cryosparc_P4_J219_002_volume_map_sharp.mrc z flip as #7, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #6
> rename CS_P4_J219_sharp_flip id #6
Missing or invalid "models" argument: invalid models specifier
> rename #7 CS_P4_J219_sharp_flip id #6
> save CS_P4_J219_sharp_flip.mrc #6
> show #!3 models
> select add #6
2 models selected
> view matrix models
> #6,0.55385,-0.83087,-0.054,184.1,0.82508,0.55638,-0.098423,-37.993,0.11182,0.009957,0.99368,-50.391
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.55385,-0.83087,-0.054,173.54,0.82508,0.55638,-0.098423,-43.189,0.11182,0.009957,0.99368,-15.893
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.43591,-0.88398,-0.16899,334.46,0.87276,-0.46105,0.1604,51.515,-0.2197,-0.077569,0.97248,45.011
> fitmap #6 inMap #3
Fit map CS_P4_J219_sharp_flip.mrc in map CS_P4_J216_class_2_sharp_flip.mrc
using 3507 points
correlation = 0.9414, correlation about mean = 0.4694, overlap = 2583
steps = 72, shift = 3.53, angle = 4.05 degrees
Position of CS_P4_J219_sharp_flip.mrc (#6) relative to
CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.45821390 -0.85833568 -0.23086770 342.48607306
0.85407817 -0.49711214 0.15306861 63.33623820
-0.24615139 -0.12704090 0.96086946 56.91191433
Axis -0.16142412 0.00880783 0.98684582
Axis point 157.30567711 132.03749632 0.00000000
Rotation angle (degrees) 119.81679395
Shift along axis 1.43562700
> select subtract #6
Nothing selected
> hide #!3 models
Unsupported scale factor (0.000000) detected on Display1
[Repeated 2 time(s)]
> hide #!6 models
> show #!3 models
> show #!6 models
> hide #!6 models
> color #3 #B1DCFC
> save P4_J216_class_2_sharp.png supersample 3 transparentBackground true
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!3 models
> show #!6 models
> hide #!3 models
> hide #!6 models
> show #!3 models
> color #3 #AFDBFF
> hide #!3 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> color #3 #99BFE5
> hide #!6 models
> view P1
> save P4_J216_class_2_sharp.png supersample 3 transparentBackground true
> hide #!3 models
> show #!6 models
> ui mousemode right translate
> save P4_J219_NU_sharp_flip.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260430_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J243_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J243_003_volume_map_sharp.mrc as #7, grid size 80,80,80,
pixel 3.32, shown at level 1.1, step 1, values float32
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.34351,0.88804,0.30558,-69.154,0.93106,-0.36463,0.013018,61.425,0.12299,0.28005,-0.95208,168.53
> view matrix models
> #7,-0.72211,0.66266,0.19859,108.59,0.68148,0.73076,0.039546,-55.441,-0.11892,0.16389,-0.97928,217.85
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.72211,0.66266,0.19859,107.8,0.68148,0.73076,0.039546,-63.119,-0.11892,0.16389,-0.97928,255.33
> view matrix models
> #7,-0.72211,0.66266,0.19859,116.79,0.68148,0.73076,0.039546,-56.849,-0.11892,0.16389,-0.97928,258.31
> fitmap #7 inMap #6
Fit map cryosparc_P4_J243_003_volume_map_sharp.mrc in map
CS_P4_J219_sharp_flip.mrc using 5116 points
correlation = 0.9377, correlation about mean = 0.7097, overlap = 1.519e+04
steps = 76, shift = 2.16, angle = 10.6 degrees
Position of cryosparc_P4_J243_003_volume_map_sharp.mrc (#7) relative to
CS_P4_J219_sharp_flip.mrc (#6) coordinates:
Matrix rotation and translation
0.96909604 0.16642828 0.18208375 -39.18937125
0.15922720 -0.98578684 0.05358170 236.77616183
0.18841328 -0.02293313 -0.98182203 241.04145354
Axis -0.99224103 -0.08208102 -0.09338329
Axis point 0.00000000 122.34870623 120.06626952
Rotation angle (degrees) 177.79032322
Shift along axis -3.05877231
> select subtract #7
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,-0.62422,0.77517,0.097247,102.65,0.77737,0.62868,-0.021408,-52.876,-0.077732,0.062233,-0.99503,269.09
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.32669,-0.93485,0.13901,287.37,-0.94032,0.30667,-0.14745,222.88,0.095218,-0.17888,-0.97925,277.34
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.32669,-0.93485,0.13901,281.61,-0.94032,0.30667,-0.14745,233.21,0.095218,-0.17888,-0.97925,273.65
> fitmap #7 inMap #6
Fit map cryosparc_P4_J243_003_volume_map_sharp.mrc in map
CS_P4_J219_sharp_flip.mrc using 5116 points
correlation = 0.9419, correlation about mean = 0.7222, overlap = 1.551e+04
steps = 56, shift = 3.52, angle = 7.25 degrees
Position of cryosparc_P4_J243_003_volume_map_sharp.mrc (#7) relative to
CS_P4_J219_sharp_flip.mrc (#6) coordinates:
Matrix rotation and translation
-0.62645631 0.77281267 0.10155321 101.66723571
0.77509514 0.63140454 -0.02357570 -50.90352474
-0.08234076 0.06394425 -0.99455072 266.97848709
Axis 0.42971205 0.90289643 0.01120665
Axis point 70.49413903 0.00000000 130.93970837
Rotation angle (degrees) 174.15511884
Shift along axis 0.71895896
> select subtract #7
Nothing selected
> hide #!6 models
> volume #7 level 1.41
> color #7 #99BFE5
> view P1
> close #7
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J244_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J244_003_volume_map_sharp.mrc as #7, grid size 80,80,80,
pixel 3.32, shown at level 1.05, step 1, values float32
> show #!6 models
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.71966,-0.6805,-0.13788,149.49,-0.69285,-0.71678,-0.078638,342.79,-0.045318,0.15212,-0.98732,223.99
> hide #!6 models
> show #!6 models
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.71966,-0.6805,-0.13788,149.4,-0.69285,-0.71678,-0.078638,338.98,-0.045318,0.15212,-0.98732,258.19
> select subtract #7
Nothing selected
> hide #!6 models
> volume flip #7
Opened cryosparc_P4_J244_003_volume_map_sharp.mrc z flip as #8, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #7
> rename #8 CS_P4_J244_sharp_flip id #7
> save CS_P4_J244_sharp_flip.mrc #7
> color #7 #99BFE5
> volume #7 level 1.156
> save CS_P4_J244_sharp_flip.mrc #7
> save P4_J244_NU_sharp_flip.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_00_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size
128,128,128, pixel 2.08, shown at level 0.192, step 1, values float32
> hide #!7 models
> volume #8 level 0.2208
> show #!7 models
> select add #8
2 models selected
> view matrix models #8,1,0,0,1.7912,0,1,0,4.218,0,0,1,1.8536
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.019063,-0.87425,-0.4851,301.31,0.055421,0.48537,-0.87255,194.56,0.99828,-0.010251,0.057705,27.748
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.019063,-0.87425,-0.4851,303.09,0.055421,0.48537,-0.87255,199.03,0.99828,-0.010251,0.057705,19.845
> view matrix models
> #8,0.019063,-0.87425,-0.4851,323.73,0.055421,0.48537,-0.87255,193.31,0.99828,-0.010251,0.057705,17.439
> view matrix models
> #8,0.019063,-0.87425,-0.4851,322.89,0.055421,0.48537,-0.87255,188.18,0.99828,-0.010251,0.057705,19.28
> fitmap #8 inMap #7
Fit map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc in map
CS_P4_J244_sharp_flip.mrc using 14754 points
correlation = 0.481, correlation about mean = 0.07756, overlap = 1756
steps = 112, shift = 13.3, angle = 15.3 degrees
Position of cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) relative to
CS_P4_J244_sharp_flip.mrc (#7) coordinates:
Matrix rotation and translation
0.05423844 -0.87969653 0.47243223 170.87663448
0.10002936 0.47553549 0.87399092 -59.90285646
-0.99350507 -0.00014682 0.11378778 232.31099922
Axis -0.44417982 0.74489379 0.49783284
Axis point 199.16697689 -0.00000000 41.59458970
Rotation angle (degrees) 100.26604714
Shift along axis -4.86917491
> select subtract #8
Nothing selected
> hide #!7 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_01_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.08, shown at level 0.178, step 1, values float32
> hide #!8 models
> volume #9 level 0.1464
> show #!8 models
> select add #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.01099,0.99675,0.079835,4.9565,0.1314,-0.080587,0.98805,-14.68,0.99127,-0.00036851,-0.13186,9.8
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.01099,0.99675,0.079835,10.903,0.1314,-0.080587,0.98805,5.6709,0.99127,-0.00036851,-0.13186,51.786
> view matrix models
> #9,0.01099,0.99675,0.079835,4.7224,0.1314,-0.080587,0.98805,-1.1935,0.99127,-0.00036851,-0.13186,45.788
> fitmap #9 inMap #8
Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 29766 points
correlation = 0.8496, correlation about mean = 0.3082, overlap = 1328
steps = 284, shift = 18.3, angle = 53.9 degrees
Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to
cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99575722 -0.02668322 0.08806571 -8.52134797
-0.09034177 -0.46538978 0.88048323 89.22150736
0.01749075 -0.88470354 -0.46582584 307.69453028
Axis -0.99855360 0.03992375 -0.03601119
Axis point 0.00000000 137.23273941 127.10917488
Rotation angle (degrees) 117.88699495
Shift along axis 0.99063260
> select subtract #9
Nothing selected
> hide #!8 models
> hide #!9 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_02_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
> select add #10
2 models selected
> show #!9 models
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.17462,0.93232,0.31669,19.869,0.21917,0.35036,-0.91061,163.76,-0.95993,-0.089597,-0.26552,316.03
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.17462,0.93232,0.31669,8.7975,0.21917,0.35036,-0.91061,193.69,-0.95993,-0.089597,-0.26552,324.3
> view matrix models
> #10,-0.17462,0.93232,0.31669,5.0809,0.21917,0.35036,-0.91061,186.44,-0.95993,-0.089597,-0.26552,324.52
> fitmap #10 inMap #9
Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20970 points
correlation = 0.8182, correlation about mean = 0.3079, overlap = 1048
steps = 212, shift = 18, angle = 29.3 degrees
Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative
to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates:
Matrix rotation and translation
-0.92160797 -0.37293352 0.10751436 286.70013052
-0.37621404 0.79028143 -0.48365097 141.61699812
0.09540306 -0.48618500 -0.86863249 299.79876520
Axis -0.19795503 0.94611818 -0.25626978
Axis point 158.67244900 0.00000000 168.59386356
Rotation angle (degrees) 179.63327476
Shift along axis 0.40332117
> select subtract #10
Nothing selected
> hide #!9 models
> hide #!10 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_03_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.08, shown at level 0.218, step 1, values float32
> volume #11 level 0.1502
> show #!10 models
> select add #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.73904,-0.47164,0.48101,26.135,-0.11204,0.61802,0.77814,-47.481,-0.66427,-0.62897,0.4039,253.49
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.73904,-0.47164,0.48101,5.5926,-0.11204,0.61802,0.77814,-27.642,-0.66427,-0.62897,0.4039,266.06
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.56676,0.0073102,0.82385,78.335,0.19153,-0.97139,0.14038,216.5,0.80131,0.23736,0.54915,-63.542
> select subtract #11
Nothing selected
> fitmap #11 inMap #10
Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 45754 points
correlation = 0.7333, correlation about mean = -0.04196, overlap = 1268
steps = 132, shift = 23.8, angle = 15.3 degrees
Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative
to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.26691235 0.13508665 -0.95420616 300.80664915
-0.90776913 -0.36770197 0.20186745 274.07355373
-0.32359389 0.92007981 0.22077169 18.93443182
Axis 0.50771970 -0.44579332 -0.73721708
Axis point 236.02557416 49.14154001 0.00000000
Rotation angle (degrees) 134.98497404
Shift along axis 16.58651491
> hide #!10 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_04_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.08, shown at level 0.261, step 1, values float32
> show #!10 models
> hide #!10 models
> select add #12
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,-3.7479,0,1,0,3.9168,0,0,1,20.991
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.79132,-0.13023,0.59737,-27.645,0.22144,0.97176,-0.081485,-12.263,-0.56989,0.19676,0.79781,93.603
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.79132,-0.13023,0.59737,-50.124,0.22144,0.97176,-0.081485,3.5285,-0.56989,0.19676,0.79781,102.68
> view matrix models
> #12,0.79132,-0.13023,0.59737,-48.335,0.22144,0.97176,-0.081485,2.277,-0.56989,0.19676,0.79781,101.98
> view matrix models
> #12,0.79132,-0.13023,0.59737,-41.566,0.22144,0.97176,-0.081485,-1.9637,-0.56989,0.19676,0.79781,101.41
> fitmap #12 inMap #11
Fit map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20956 points
correlation = 0.8514, correlation about mean = 0.04285, overlap = 1430
steps = 80, shift = 7.16, angle = 11.7 degrees
Position of cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) relative
to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates:
Matrix rotation and translation
-0.93263188 0.26201641 0.24808299 197.07280134
-0.29117819 -0.95255879 -0.08858337 308.05329962
0.21310334 -0.15485204 0.96468016 17.95641726
Axis -0.11870856 0.06265985 -0.99095006
Axis point 119.69175871 140.62215054 0.00000000
Rotation angle (degrees) 163.79210928
Shift along axis -21.88556717
> select subtract #12
Nothing selected
> hide #!11 models
> volume #12 level 0.4033
> volume #12 level 0.3453
> color #8 #FCEDFF
> hide #!12 models
> show #!8 models
> hide #!8 models
> show #!9 models
> color #9 #FCEDFF
> hide #!9 models
> show #!10 models
> color #10 #FCEDFF
> hide #!10 models
> show #!11 models
> color #11 #FCEDFF
> hide #!11 models
> show #!12 models
> color #12 #99BFE5
> view P1
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!3 models
> select add #12
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.95369,-0.29732,-0.045496,35.025,0.29889,0.95373,0.032695,-17.906,0.03367,-0.044779,0.99843,26.075
> view matrix models
> #12,-0.8879,0.32078,-0.32974,233.6,0.30063,0.94715,0.1119,-26.299,0.34821,0.00022498,-0.93742,198.42
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.8879,0.32078,-0.32974,232.89,0.30063,0.94715,0.1119,-34.317,0.34821,0.00022498,-0.93742,213.72
> view matrix models
> #12,-0.8879,0.32078,-0.32974,243.25,0.30063,0.94715,0.1119,-55.273,0.34821,0.00022498,-0.93742,214.76
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.88731,0.39919,0.23093,169.34,0.40717,0.91324,-0.014156,-50.796,-0.21654,0.081466,-0.97287,283.71
> fitmap #12 inMap #3
Fit map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc in map
CS_P4_J216_class_2_sharp_flip.mrc using 12546 points
correlation = 0.9893, correlation about mean = 0.7632, overlap = 2433
steps = 124, shift = 11, angle = 27.9 degrees
Position of cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) relative
to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates:
Matrix rotation and translation
-0.62359754 0.77535022 0.09979057 101.14085164
0.77719680 0.62864768 -0.02769904 -50.42984630
-0.08420957 0.06028386 -0.99462285 268.88184712
Axis 0.43136931 0.90213001 0.00905357
Axis point 70.24601107 0.00000000 131.83510298
Rotation angle (degrees) 174.14674629
Shift along axis 0.56912319
> select subtract #12
Nothing selected
> hide #!12 models
> show #!12 models
> show #!11 models
> select add #11
2 models selected
> view matrix models
> #11,-0.37852,0.89247,0.24538,28.817,0.88041,0.42898,-0.20213,16.101,-0.28566,0.13952,-0.94812,300.03
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.37852,0.89247,0.24538,46.8,0.88041,0.42898,-0.20213,-5.6117,-0.28566,0.13952,-0.94812,300.85
> view matrix models
> #11,-0.37852,0.89247,0.24538,36.63,0.88041,0.42898,-0.20213,-16.953,-0.28566,0.13952,-0.94812,296.6
> fitmap #11 inMap #12
Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 45754 points
correlation = 0.7192, correlation about mean = 0.1299, overlap = 1714
steps = 96, shift = 6.98, angle = 12.7 degrees
Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative
to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates:
Matrix rotation and translation
0.88557701 -0.25567312 -0.38779454 99.27082409
0.32552043 0.93717068 0.12548928 -53.44589150
0.33134544 -0.23736546 0.91316364 -22.95393091
Axis -0.36530839 -0.72400286 0.58512361
Axis point 106.02252826 0.00000000 214.34257569
Rotation angle (degrees) 29.77806268
Shift along axis -11.00037360
> select subtract #11
Nothing selected
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!3 models
> show #!12 models
> hide #!11 models
> show #!10 models
> select add #10
2 models selected
> view matrix models
> #10,-0.49822,0.81176,0.30466,37.524,-0.14214,0.27015,-0.95227,247.33,-0.85532,-0.51775,-0.019207,343.36
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.013344,0.85199,0.52339,-68.961,-0.1627,-0.51831,0.83957,128.11,0.98659,-0.073951,0.14553,-15.381
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.013344,0.85199,0.52339,-45.161,-0.1627,-0.51831,0.83957,119.13,0.98659,-0.073951,0.14553,-13.578
> fitmap #10 inMap #12
Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20970 points
correlation = 0.7101, correlation about mean = 0.02358, overlap = 908.6
steps = 80, shift = 7.98, angle = 9.33 degrees
Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative
to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates:
Matrix rotation and translation
-0.35385865 -0.88893073 0.29083707 267.80089120
-0.02210060 0.31881642 0.94755878 -31.84809054
-0.93503776 0.32887420 -0.13246184 232.75133151
Axis -0.38099533 0.75491227 0.53380711
Axis point 205.22642342 0.00000000 36.94010088
Rotation angle (degrees) 125.71487620
Shift along axis -1.82908632
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.12287,-0.47662,0.87048,95.543,0.19038,-0.87215,-0.45067,269.26,0.97399,0.11035,0.1979,-37.789
> select subtract #10
Nothing selected
> hide #!12 models
> show #!11 models
> show #!12 models
> hide #!10 models
> hide #!12 models
> show #!10 models
> select add #10
2 models selected
> view matrix models
> #10,-0.38685,-0.21971,0.89558,99.669,-0.053858,-0.96416,-0.2598,294.54,0.92057,-0.14874,0.36115,-16.709
> fitmap #10 inMap #11
Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20970 points
correlation = 0.8482, correlation about mean = 0.1221, overlap = 870.1
steps = 88, shift = 3.31, angle = 12.5 degrees
Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative
to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates:
Matrix rotation and translation
-0.32110732 -0.67353914 -0.66575904 357.49560201
0.09667773 -0.72262784 0.68444314 122.97291760
-0.94209527 0.15541563 0.29715733 219.46626263
Axis -0.54292343 0.28359472 0.79044809
Axis point 234.55310205 82.20310947 0.00000000
Rotation angle (degrees) 150.84311237
Shift along axis 14.25842210
> view matrix models
> #10,-0.30509,0.38504,-0.87101,233.77,0.18733,0.92101,0.34153,-54.422,0.93372,-0.058973,-0.35312,61.617
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.30509,0.38504,-0.87101,240.35,0.18733,0.92101,0.34153,-58.712,0.93372,-0.058973,-0.35312,49.559
> view matrix models
> #10,-0.30509,0.38504,-0.87101,238.16,0.18733,0.92101,0.34153,-58.03,0.93372,-0.058973,-0.35312,51.895
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.36524,0.52001,-0.77213,217.65,0.08187,0.84416,0.5298,-55.56,0.9273,0.13029,-0.3509,28.264
> fitmap #10 inMap #11
Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20970 points
correlation = 0.8485, correlation about mean = 0.1929, overlap = 854.7
steps = 140, shift = 18.2, angle = 22.5 degrees
Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative
to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates:
Matrix rotation and translation
-0.33967352 0.22689098 0.91276633 25.87088295
0.00914596 0.97121791 -0.23801704 28.63290177
-0.94049893 -0.07249996 -0.33197214 335.97765353
Axis 0.08835402 0.98928424 -0.11623361
Axis point 129.11230783 0.00000000 160.33867701
Rotation angle (degrees) 110.50039702
Shift along axis -8.44002041
> view matrix models
> #10,-0.23006,0.48061,-0.84622,212.13,0.22993,0.87177,0.43261,-89.291,0.94562,-0.095042,-0.31107,58.162
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.23006,0.48061,-0.84622,206.51,0.22993,0.87177,0.43261,-81.849,0.94562,-0.095042,-0.31107,43.385
> view matrix models
> #10,-0.23006,0.48061,-0.84622,209.88,0.22993,0.87177,0.43261,-83.853,0.94562,-0.095042,-0.31107,44.292
> select subtract #10
Nothing selected
> hide #!10 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!9 models
> show #!10 models
> select add #9
2 models selected
> view matrix models
> #9,0.18919,0.68161,-0.70683,127.56,-0.072128,0.72753,0.68227,-34.663,0.97929,-0.078095,0.1868,-5.196
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.094504,0.99539,-0.016524,13.65,-0.46578,0.02954,-0.88441,305.71,-0.87984,0.091276,0.46642,193.56
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.094504,0.99539,-0.016524,15.801,-0.46578,0.02954,-0.88441,306.87,-0.87984,0.091276,0.46642,176.78
> view matrix models
> #9,0.094504,0.99539,-0.016524,12.042,-0.46578,0.02954,-0.88441,307.73,-0.87984,0.091276,0.46642,167.03
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.21351,-0.97318,0.085687,220.62,-0.11603,0.061829,0.99132,14.069,-0.97003,-0.2216,-0.099713,290.21
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.21351,-0.97318,0.085687,223.99,-0.11603,0.061829,0.99132,9.6501,-0.97003,-0.2216,-0.099713,279.71
> fitmap #9 inMap #10
Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 29766 points
correlation = 0.8261, correlation about mean = 0.3518, overlap = 1268
steps = 228, shift = 10.5, angle = 43.8 degrees
Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.79231406 -0.50183310 0.34698987 259.09489231
0.60835065 -0.60661249 0.51179172 70.83831660
-0.04634564 0.61659129 0.78591810 -47.09681091
Axis 0.08862868 0.33264264 0.93887903
Axis point 119.55771099 88.88471782 0.00000000
Rotation angle (degrees) 143.75577737
Shift along axis 2.30887434
> select subtract #9
Nothing selected
> hide #!9 models
> hide #!10 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!9 models
> show #!9 models
> select add #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.57009,0.77789,0.26434,-76.801,0.087184,0.26265,-0.96094,232.01,-0.81694,0.57087,0.081917,150.81
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.57009,0.77789,0.26434,-65.422,0.087184,0.26265,-0.96094,221.32,-0.81694,0.57087,0.081917,140.75
> view matrix models
> #8,0.57009,0.77789,0.26434,-76.259,0.087184,0.26265,-0.96094,220.33,-0.81694,0.57087,0.081917,139.28
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.35163,-0.43011,0.83148,20.753,0.096433,0.90012,0.42483,-70.009,-0.93116,-0.069204,0.35799,194.15
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.35163,-0.43011,0.83148,32.249,0.096433,0.90012,0.42483,-69.075,-0.93116,-0.069204,0.35799,199.19
> fitmap #8 inMap #9
Fit map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 14754 points
correlation = 0.886, correlation about mean = 0.3322, overlap = 930.7
steps = 164, shift = 11.7, angle = 31.5 degrees
Position of cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) relative to
cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.99392076 -0.10814474 0.02064566 12.78899705
-0.02517844 -0.40582068 -0.91360584 308.93876287
0.10718010 0.90753198 -0.40607651 52.31471926
Axis 0.99784036 -0.04741407 0.04545901
Axis point 0.00000000 137.80284162 126.13315110
Rotation angle (degrees) 114.14129203
Shift along axis 0.49150880
> select subtract #8
Nothing selected
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> view P1
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!8 models
> show #!12 models
> view P1
> select add #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.17056,0.37082,0.91291,-61.936,0.033776,0.92374,-0.38153,50.195,-0.98477,0.095906,0.14502,217.51
> select subtract #8
Nothing selected
> hide #!12 models
> show #!9 models
> select add #9
2 models selected
> view matrix models
> #9,0.22431,-0.86548,-0.44791,277.63,0.10958,-0.43431,0.89407,50.356,-0.96834,-0.24963,-0.0025846,282.76
> fitmap #9 inMap #8
Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 29766 points
correlation = 0.8496, correlation about mean = 0.3079, overlap = 1328
steps = 196, shift = 4.92, angle = 23.1 degrees
Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to
cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99577299 -0.02696715 0.08780046 -8.42294333
-0.09023986 -0.46536786 0.88050527 89.20116331
0.01711480 -0.88470646 -0.46583426 307.74421532
Axis -0.99855897 0.03998603 -0.03579261
Axis point 0.00000000 137.24012810 127.13677639
Rotation angle (degrees) 117.88604570
Shift along axis 0.96263749
> select subtract #9
Nothing selected
> select add #9
2 models selected
> select subtract #9
Nothing selected
> hide #!8 models
> hide #!9 models
> show #!9 models
> show #!10 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!9 models
> select add #10
2 models selected
> view matrix models
> #10,-0.15057,0.45945,-0.87535,204.11,-0.21614,0.84872,0.48265,-19.059,0.96468,0.26187,-0.028487,-39.785
> fitmap #10 inMap #8
Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 20970 points
correlation = 0.8656, correlation about mean = 0.3963, overlap = 1232
steps = 148, shift = 6.34, angle = 30.8 degrees
Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative
to cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates:
Matrix rotation and translation
-0.99459983 0.06769619 -0.07866640 263.08124995
0.09074118 0.93510189 -0.34256458 42.75279763
0.05037079 -0.34785296 -0.93619501 298.73878944
Axis -0.04031220 -0.98362390 0.17566718
Axis point 125.67832095 0.00000000 157.57753081
Rotation angle (degrees) 176.23911220
Shift along axis -0.17945663
> show #!8 models
> hide #!9 models
> select subtract #10
Nothing selected
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!11 models
> hide #!10 models
> show #!10 models
> select add #11
2 models selected
> view matrix models
> #11,0.83789,-0.53148,-0.12435,93.216,-0.53452,-0.84509,0.010318,306.1,-0.11057,0.05782,-0.99219,291.46
> view matrix models
> #11,0.87567,0.38049,0.29737,-84.014,0.47018,-0.53126,-0.70477,229.85,-0.11018,0.75696,-0.64411,156.03
> view matrix models
> #11,0.99273,0.070823,-0.097356,-6.1982,0.016369,-0.88055,-0.47367,302.86,-0.11927,0.46863,-0.87531,225.51
> fitmap #11 inMap #10
Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 45754 points
correlation = 0.7386, correlation about mean = -0.02581, overlap = 1355
steps = 168, shift = 17.3, angle = 31.8 degrees
Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative
to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.38917965 0.05095816 -0.91975131 323.90582539
-0.15837916 -0.98730156 0.01231516 285.52055130
-0.90744434 0.15046225 0.39230839 175.68159882
Axis 0.55013716 -0.04900950 -0.83363492
Axis point 230.74773970 125.72052254 0.00000000
Rotation angle (degrees) 172.78707980
Shift along axis 17.74509610
> select subtract #11
Nothing selected
> hide #!11 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> view P1
> show #!12 models
> ui mousemode right translate
> save P4_J242_class_4_sharp.png supersample 3 transparentBackground true
> hide #!12 models
> show #!11 models
> save P4_J242_class_3_sharp.png supersample 3 transparentBackground true
> hide #!11 models
> show #!10 models
> save P4_J242_class_2_sharp.png supersample 3 transparentBackground true
> hide #!10 models
> show #!9 models
> view P1
[Repeated 1 time(s)]
> save P4_J242_class_1_sharp.png supersample 3 transparentBackground true
> hide #!9 models
> show #!8 models
> save P4_J242_class_0_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
Unsupported scale factor (0.000000) detected on Display1
[Repeated 2 time(s)]
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J117_class_00_00162_volume_sharp.mrc"
Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32
> hide #!8 models
> select add #13
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #13,1,0,0,6.2015,0,1,0,0.69431,0,0,1,-17.516
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.13264,-0.68512,-0.71625,337.99,0.0019176,-0.72281,0.69104,120.39,-0.99116,0.090284,0.097186,224.71
> view matrix models
> #13,0.0040424,0.12352,-0.99233,257.27,0.14964,-0.98124,-0.12153,245.92,-0.98873,-0.148,-0.02245,270.75
> select subtract #13
Nothing selected
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!10 models
> fitmap #13 inMap #10
Fit map cryosparc_P4_J117_class_00_00162_volume_sharp.mrc in map
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 20961 points
correlation = 0.8109, correlation about mean = 0.2077, overlap = 1054
steps = 92, shift = 12.7, angle = 18.1 degrees
Position of cryosparc_P4_J117_class_00_00162_volume_sharp.mrc (#13) relative
to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.98193657 -0.07856914 0.17212633 243.32837219
0.00195692 -0.91387700 -0.40598645 309.66348462
0.18920029 -0.39831610 0.89752300 41.87114917
Axis 0.09277951 -0.20652448 0.97403265
Axis point 116.38449758 161.85402651 0.00000000
Rotation angle (degrees) 177.63092236
Shift along axis -0.59333628
> hide #!10 models
> hide #!13 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J117_class_01_00162_volume_sharp.mrc"
Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32
> select add #14
2 models selected
> view matrix models
> #14,-0.39254,-0.77748,0.49135,234.79,-0.04345,-0.51796,-0.8543,320.26,0.91871,-0.3567,0.16954,27.288
> view matrix models
> #14,-0.061348,0.89979,0.432,-25.376,-0.288,-0.43036,0.85548,115.2,0.95566,-0.071931,0.28554,-30.976
> view matrix models
> #14,-0.046716,0.65995,-0.74985,161.94,-0.070464,0.74662,0.6615,-44.914,0.99642,0.08374,0.011624,-20.712
> select subtract #14
Nothing selected
> show #!13 models
> fitmap #14 inMap #13
Fit map cryosparc_P4_J117_class_01_00162_volume_sharp.mrc in map
cryosparc_P4_J117_class_00_00162_volume_sharp.mrc using 20968 points
correlation = 0.846, correlation about mean = 0.3465, overlap = 1110
steps = 132, shift = 18.5, angle = 19.5 degrees
Position of cryosparc_P4_J117_class_01_00162_volume_sharp.mrc (#14) relative
to cryosparc_P4_J117_class_00_00162_volume_sharp.mrc (#13) coordinates:
Matrix rotation and translation
-0.99955515 0.02982234 0.00035424 260.68209471
-0.00628473 -0.19900464 -0.97997839 284.54003350
-0.02915475 -0.97954468 0.19910354 244.04930876
Axis 0.00930049 0.63278447 -0.77427212
Axis point 133.98017190 240.03303746 0.00000000
Rotation angle (degrees) 178.66392593
Shift along axis -6.48359029
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J117_class_02_00162_volume_sharp.mrc"
Opened cryosparc_P4_J117_class_02_00162_volume_sharp.mrc as #15, grid size
128,128,128, pixel 2.08, shown at level 0.251, step 1, values float32
> hide #!13 models
> select add #14
2 models selected
> show #!12 models
> select subtract #14
Nothing selected
> hide #!14 models
> select add #15
2 models selected
> view matrix models
> #15,-0.98221,0.18526,0.030552,219.51,0.18651,0.98144,0.044675,-26.394,-0.021708,0.049578,-0.99853,243.73
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.98221,0.18526,0.030552,234.62,0.18651,0.98144,0.044675,-36.86,-0.021708,0.049578,-0.99853,271.78
> fitmap #15 inMap #12
Fit map cryosparc_P4_J117_class_02_00162_volume_sharp.mrc in map
cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20967 points
correlation = 0.781, correlation about mean = 0.07908, overlap = 1573
steps = 76, shift = 10.9, angle = 6.65 degrees
Position of cryosparc_P4_J117_class_02_00162_volume_sharp.mrc (#15) relative
to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates:
Matrix rotation and translation
0.82536305 0.56130744 0.06090799 -57.36751075
-0.56057744 0.82755504 -0.03009290 101.38226037
-0.06729608 -0.00930608 0.99768964 1.14989876
Axis 0.01840555 0.11351744 -0.99336550
Axis point 134.55599767 144.37243816 0.00000000
Rotation angle (degrees) 34.38068857
Shift along axis 9.31050435
> volume flip #15
Opened cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip as #16, grid
size 128,128,128, pixel 2.08, shown at step 1, values float32
> close #15
> select add #16
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.81511,-0.57721,0.04929,312.41,0.52972,-0.77708,-0.33992,218.14,0.2345,-0.25096,0.93916,8.6526
> fitmap #15 inMap #12
No atoms or maps for #15
> fitmap #16 inMap #12
Fit map cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip in map
cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20967 points
correlation = 0.9777, correlation about mean = 0.7437, overlap = 2747
steps = 108, shift = 14.1, angle = 17.5 degrees
Position of cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip (#16)
relative to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12)
coordinates:
Matrix rotation and translation
0.94024990 -0.32652551 -0.09649458 65.60674301
-0.33221344 -0.94188358 -0.04989541 307.74881291
-0.07459454 0.07897095 -0.99408211 253.25354142
Axis 0.98493295 -0.16738329 -0.04347315
Axis point 0.00000000 155.23786381 133.19610246
Rotation angle (degrees) 176.24909728
Shift along axis 2.09650544
> select subtract #16
Nothing selected
> rename #16 CS_P4_J117_class_02_sharp_flip.mrc id #15
> save CS_P4_J117_class_02_sharp_flip.mrc #15
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J117_class_03_00162_volume_sharp.mrc"
Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32
> hide #!12 models
> hide #!15 models
> select add #16
2 models selected
> show #!14 models
> view matrix models
> #16,0.00021536,0.34795,0.93751,-37.63,0.50671,0.80821,-0.30007,0.053261,-0.86212,0.47511,-0.17613,183.13
> hide #!14 models
> view matrix models
> #16,0.63015,0.10301,-0.76961,125.95,-0.74582,0.35606,-0.56301,261.02,0.21603,0.92877,0.3012,-81.743
> view matrix models
> #16,0.63277,-0.43368,-0.64151,190.37,0.75188,0.14602,0.64293,-47.242,-0.18515,-0.88916,0.41847,227.83
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!11 models
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.63277,-0.43368,-0.64151,206.09,0.75188,0.14602,0.64293,-70.694,-0.18515,-0.88916,0.41847,249.05
> view matrix models
> #16,0.63277,-0.43368,-0.64151,204.5,0.75188,0.14602,0.64293,-75.196,-0.18515,-0.88916,0.41847,240.94
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.30976,-0.38252,-0.87047,346.06,0.94397,-0.2334,-0.23335,63.654,-0.1139,-0.89398,0.43339,230.67
> fitmap #16 inMap #11
Fit map cryosparc_P4_J117_class_03_00162_volume_sharp.mrc in map
cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20958 points
correlation = 0.9023, correlation about mean = 0.3197, overlap = 1117
steps = 184, shift = 6.54, angle = 53.8 degrees
Position of cryosparc_P4_J117_class_03_00162_volume_sharp.mrc (#16) relative
to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates:
Matrix rotation and translation
0.41743274 -0.19488532 -0.88756388 222.32976103
-0.90862481 -0.10271919 -0.40478358 322.57606660
-0.01228347 0.97543246 -0.21995599 21.59894000
Axis 0.77392148 -0.49079151 -0.40021149
Axis point 0.00000000 222.40854643 197.20887777
Rotation angle (degrees) 116.91198346
Shift along axis 5.10403978
> select subtract #16
Nothing selected
> hide #!11 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J117_class_04_00162_volume_sharp.mrc"
Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32
> hide #!16 models
> select add #17
2 models selected
> show #!13 models
> hide #!13 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!17 models
> show #!17 models
> view matrix models
> #17,-0.0034658,-0.079884,-0.9968,294.42,-0.15421,0.98492,-0.078396,35.543,0.98803,0.15344,-0.015732,-30.795
> fitmap #17 inMap #10
Fit map cryosparc_P4_J117_class_04_00162_volume_sharp.mrc in map
cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 20958 points
correlation = 0.8416, correlation about mean = 0.3036, overlap = 1170
steps = 148, shift = 13.9, angle = 32.2 degrees
Position of cryosparc_P4_J117_class_04_00162_volume_sharp.mrc (#17) relative
to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.73519379 0.67627298 0.04631360 -60.93633283
-0.67522557 0.73664284 -0.03778583 134.15115598
-0.05967011 -0.00349222 0.99821205 3.94076312
Axis 0.02528875 0.07815439 -0.99662047
Axis point 141.29888305 145.62167557 0.00000000
Rotation angle (degrees) 42.69072745
Shift along axis 5.01605257
> select subtract #17
Nothing selected
> hide #!10 models
> show #!10 models
> hide #!17 models
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> show #!13 models
> hide #!10 models
> color #13 #FCEDFF
> hide #!13 models
> show #!14 models
> color #14 #FCEDFF
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!16 models
> color #16 #FCEDFF
> hide #!16 models
> show #!17 models
> color #17 #FCEDFF
> show #!15 models
> hide #!17 models
> color #15 #99BFE5
> volume #15 level 0.3349
> ui mousemode right translate
> view P1
[Repeated 1 time(s)]
> save P4_J117_class_2_sharp.png supersample 3 transparentBackground true
> hide #!15 models
> show #!13 models
> save P4_J117_class_0_sharp.png supersample 3 transparentBackground true
> hide #!13 models
> show #!14 models
> save P4_J117_class_1_sharp.png supersample 3 transparentBackground true
> hide #!14 models
> show #!16 models
> save P4_J117_class_3_sharp.png supersample 3 transparentBackground true
> hide #!16 models
> show #!17 models
> save P4_J117_class_4_sharp.png supersample 3 transparentBackground true
[Repeated 1 time(s)]
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J120_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J120_002_volume_map_sharp.mrc as #18, grid size 80,80,80,
pixel 3.32, shown at level 1.08, step 1, values float32
> hide #!17 models
> show #!15 models
> select add #18
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.9199,0.35329,0.17023,-57.439,0.37414,-0.92071,-0.11099,219.04,0.11752,0.16579,-0.97913,208.75
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.9199,0.35329,0.17023,-56.147,0.37414,-0.92071,-0.11099,218.08,0.11752,0.16579,-0.97913,234.23
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.47537,0.87487,0.092902,-59.652,0.86989,-0.48319,0.099115,73.008,0.1316,0.033698,-0.99073,251.23
> volume flip #18
Opened cryosparc_P4_J120_002_volume_map_sharp.mrc z flip as #19, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> select subtract #18
Nothing selected
> close #18
> select add #19
2 models selected
> view matrix models
> #19,0.011836,0.9987,-0.049536,1.5471,-0.96239,0.024824,0.27053,210.58,0.27141,0.044471,0.96144,-38.44
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.011836,0.9987,-0.049536,5.1894,-0.96239,0.024824,0.27053,209.75,0.27141,0.044471,0.96144,-23.291
> fitmap #19 inMap #15
Fit map cryosparc_P4_J120_002_volume_map_sharp.mrc z flip in map
CS_P4_J117_class_02_sharp_flip.mrc using 5118 points
correlation = 0.9182, correlation about mean = 0.533, overlap = 3573
steps = 76, shift = 9.96, angle = 10.7 degrees
Position of cryosparc_P4_J120_002_volume_map_sharp.mrc z flip (#19) relative
to CS_P4_J117_class_02_sharp_flip.mrc (#15) coordinates:
Matrix rotation and translation
-0.48058823 -0.86458262 0.14673736 288.72558748
0.85464108 -0.49926017 -0.14257599 104.76974006
0.19652884 0.05688743 0.97884638 -28.97188121
Axis 0.11519876 -0.02875674 0.99292613
Axis point 115.59153027 135.80137987 0.00000000
Rotation angle (degrees) 120.03315219
Shift along axis 1.48105620
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.89305,-0.32489,-0.3113,106.99,0.34183,0.93976,-0.00013805,-25.175,0.29259,-0.10629,0.95031,-3.3753
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.89305,-0.32489,-0.3113,96.178,0.34183,0.93976,-0.00013805,-42.263,0.29259,-0.10629,0.95031,-5.1551
> fitmap #19 inMap #15
Fit map cryosparc_P4_J120_002_volume_map_sharp.mrc z flip in map
CS_P4_J117_class_02_sharp_flip.mrc using 5118 points
correlation = 0.9187, correlation about mean = 0.5356, overlap = 3578
steps = 76, shift = 8.31, angle = 8.52 degrees
Position of cryosparc_P4_J120_002_volume_map_sharp.mrc z flip (#19) relative
to CS_P4_J117_class_02_sharp_flip.mrc (#15) coordinates:
Matrix rotation and translation
-0.47913034 0.85546358 0.19651003 54.96243137
-0.86530880 -0.49790427 0.05772364 303.37608678
0.14722365 -0.14238471 0.97880120 3.73022055
Axis -0.11546470 0.02843878 -0.99290440
Axis point 115.58296139 135.79077530 0.00000000
Rotation angle (degrees) 119.94157891
Shift along axis -1.42232844
> hide #!19 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!19 models
> select subtract #19
Nothing selected
> show #!15 models
> hide #!15 models
> rename #19 CS_P4_J120_sharp_flip id #18
> save CS_P4_J120_sharp_flip.mrc #18
> volume #18 level 1.185
> volume #18 level 1.639
> volume #18 step 2
> volume #18 step 1
> show #!15 models
> volume #18 level 1.559
> hide #!15 models
> volume #18 level 1.292
> view P1
> color #18 #99BFE5
> show #!17 models
> hide #!17 models
> hide #!18 models
> show #!18 models
> save P4_J120_NU_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_00_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size
128,128,128, pixel 2.08, shown at level 0.175, step 1, values float32
> select add #19
2 models selected
> hide #!18 models
> show #!18 models
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #19,1,0,0,-7.1681,0,1,0,-1.6755,0,0,1,29.407
> fitmap #19 inMap #18
Fit map cryosparc_P4_J169_class_00_00182_volume_sharp.mrc in map
CS_P4_J120_sharp_flip.mrc using 20970 points
correlation = 0.3797, correlation about mean = 0.05313, overlap = 2374
steps = 192, shift = 6.4, angle = 17.5 degrees
Position of cryosparc_P4_J169_class_00_00182_volume_sharp.mrc (#19) relative
to CS_P4_J120_sharp_flip.mrc (#18) coordinates:
Matrix rotation and translation
0.64594502 0.66965380 0.36649532 -93.21942227
-0.65111130 0.73392063 -0.19342850 149.32350272
-0.39850860 -0.11368507 0.91009153 102.27587247
Axis 0.05217441 0.50052557 -0.86414813
Axis point 153.99219258 219.18137479 0.00000000
Rotation angle (degrees) 49.83592965
Shift along axis -18.50494005
> select subtract #19
Nothing selected
> hide #!18 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_01_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size
128,128,128, pixel 2.08, shown at level 0.189, step 1, values float32
> hide #!19 models
> show #!17 models
> select add #20
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.023382,0.1088,0.99379,-27.517,0.050205,0.99268,-0.10986,9.6432,-0.99847,0.052462,0.017749,251.64
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!14 models
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.023382,0.1088,0.99379,-22.964,0.050205,0.99268,-0.10986,7.1023,-0.99847,0.052462,0.017749,242.74
> ui mousemode right "rotate selected models"
> view matrix models
> #20,-0.029978,-0.71994,-0.69339,335.92,-0.21064,-0.67357,0.70847,177,-0.9771,0.16729,-0.13145,243.19
> ui mousemode right "translate selected models"
> view matrix models
> #20,-0.029978,-0.71994,-0.69339,328.25,-0.21064,-0.67357,0.70847,170.9,-0.9771,0.16729,-0.13145,240.41
> fitmap #20 inMap #14
Fit map cryosparc_P4_J169_class_01_00182_volume_sharp.mrc in map
cryosparc_P4_J117_class_01_00162_volume_sharp.mrc using 20954 points
correlation = 0.8829, correlation about mean = 0.4124, overlap = 1200
steps = 104, shift = 14, angle = 14 degrees
Position of cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) relative
to cryosparc_P4_J117_class_01_00162_volume_sharp.mrc (#14) coordinates:
Matrix rotation and translation
-0.94773816 0.28655181 -0.14028702 243.79600144
-0.24891252 -0.93914826 -0.23673424 326.23627964
-0.19958693 -0.18944287 0.96139298 60.20896934
Axis 0.08744550 0.10965027 -0.99011621
Axis point 147.27291182 149.47535150 0.00000000
Rotation angle (degrees) 164.31164420
Shift along axis -2.52311906
> select subtract #20
Nothing selected
> hide #!14 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_02_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size
128,128,128, pixel 2.08, shown at level 0.216, step 1, values float32
> hide #!20 models
> select add #21
2 models selected
> view matrix models #21,1,0,0,-13.073,0,1,0,8.3491,0,0,1,8.6967
> ui mousemode right "rotate selected models"
> view matrix models
> #21,-0.06365,0.67952,0.73089,-53.58,-0.2928,0.68743,-0.66461,177.89,-0.95405,-0.25631,0.15521,285.48
> view matrix models
> #21,0.10048,-0.44353,0.89061,41.096,0.13793,-0.88029,-0.45395,284.46,0.98533,0.16846,-0.027275,-4.3073
> fitmap #21 inMap #20
Fit map cryosparc_P4_J169_class_02_00182_volume_sharp.mrc in map
cryosparc_P4_J169_class_01_00182_volume_sharp.mrc using 20962 points
correlation = 0.7829, correlation about mean = 0.1539, overlap = 900.6
steps = 188, shift = 21.5, angle = 32 degrees
Position of cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) relative
to cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) coordinates:
Matrix rotation and translation
-0.75680258 0.56772680 0.32393846 109.96194933
0.37589927 0.78345603 -0.49487007 56.85693302
-0.53474254 -0.25275071 -0.80632963 338.09031391
Axis 0.26532092 0.94096581 -0.21020979
Axis point 90.65236627 0.00000000 161.68382083
Rotation angle (degrees) 152.85290905
Shift along axis 11.60574300
> show #!20 models
> select subtract #21
Nothing selected
> select add #21
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.31625,-0.43913,0.84092,24.723,-0.35094,-0.87769,-0.32634,336.73,0.88138,-0.19191,-0.43168,94.219
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.23561,0.79493,-0.55908,75.399,0.21977,0.51679,0.82742,-71.321,0.94667,-0.31782,-0.052938,48.925
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.23561,0.79493,-0.55908,69.861,0.21977,0.51679,0.82742,-70.077,0.94667,-0.31782,-0.052938,40.098
> fitmap #21 inMap #20
Fit map cryosparc_P4_J169_class_02_00182_volume_sharp.mrc in map
cryosparc_P4_J169_class_01_00182_volume_sharp.mrc using 20962 points
correlation = 0.8883, correlation about mean = 0.4082, overlap = 1398
steps = 80, shift = 8.95, angle = 4.79 degrees
Position of cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) relative
to cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) coordinates:
Matrix rotation and translation
-0.99875153 -0.02706229 -0.04198798 281.31180443
0.03395891 -0.98426911 -0.17338138 286.61926959
-0.03663538 -0.17459079 0.98395929 28.58358251
Axis -0.01973976 -0.08736459 0.99598081
Axis point 138.73615561 146.72655614 0.00000000
Rotation angle (degrees) 178.24454217
Shift along axis -2.12470384
> select subtract #21
Nothing selected
> hide #!20 models
> hide #!21 models
> show #!21 models
> show #!20 models
> hide #!21 models
> show #!21 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_03_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc as #22, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
> hide #!20 models
> hide #!21 models
> select add #22
2 models selected
> show #!18 models
> ui mousemode right "rotate selected models"
> view matrix models
> #22,0.80286,-0.54835,0.23395,74.113,-0.54307,-0.83458,-0.092472,336.96,0.24595,-0.052807,-0.96784,209.56
> view matrix models
> #22,0.23802,0.97115,0.01476,-30.605,0.97056,-0.2384,0.03436,32.801,0.036887,0.0061467,-0.9993,233.87
> ui mousemode right "translate selected models"
> view matrix models
> #22,0.23802,0.97115,0.01476,-35.135,0.97056,-0.2384,0.03436,31.843,0.036887,0.0061467,-0.9993,265.72
> view matrix models
> #22,0.23802,0.97115,0.01476,-30.091,0.97056,-0.2384,0.03436,32.303,0.036887,0.0061467,-0.9993,265.71
> select subtract #22
Nothing selected
> hide #!18 models
> volume flip #22
Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip as #23, grid
size 128,128,128, pixel 2.08, shown at step 1, values float32
> close #22
> show #!21 models
> hide #!21 models
> show #!18 models
> select add #23
2 models selected
> view matrix models
> #23,0.23802,0.97115,0.01476,-34.192,0.97056,-0.2384,0.03436,27.412,0.036887,0.0061467,-0.9993,278.73
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.23315,-0.92003,-0.31494,337.04,0.93397,-0.30205,0.19095,18.61,-0.27081,-0.24962,0.92971,78.293
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.23315,-0.92003,-0.31494,335.86,0.93397,-0.30205,0.19095,18.866,-0.27081,-0.24962,0.92971,88.616
> fitmap #23 inMap #18
Fit map cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip in map
CS_P4_J120_sharp_flip.mrc using 20952 points
correlation = 0.9077, correlation about mean = 0.6695, overlap = 1.202e+04
steps = 60, shift = 4.34, angle = 10.2 degrees
Position of cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip (#23)
relative to CS_P4_J120_sharp_flip.mrc (#18) coordinates:
Matrix rotation and translation
0.17479617 -0.97573598 0.13185442 219.49728105
0.98179238 0.18284123 0.05150543 -32.00811477
-0.07436413 0.12045072 0.98993010 -9.54926019
Axis 0.03500529 0.10470244 0.99388733
Axis point 128.78581299 116.22335978 0.00000000
Rotation angle (degrees) 79.99211268
Shift along axis -5.15865059
> select subtract #23
Nothing selected
> hide #!18 models
> rename #23 CS_P4_J169_class_03_sharp_flip id #22
> save CS_P4_J169_class_03_sharp_flip.mrc #22
> show #!21 models
> hide #!21 models
> show #!18 models
> hide #!18 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_04_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size
128,128,128, pixel 2.08, shown at level 0.171, step 1, values float32
> hide #!22 models
> show #!21 models
> select add #23
2 models selected
> view matrix models #23,1,0,0,62.54,0,1,0,-0.93224,0,0,1,-9.0713
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.11131,-0.99321,-0.033862,304.62,-0.95598,-0.11633,0.2694,223.09,-0.27151,0.0023841,-0.96243,297.1
> view matrix models
> #23,0.14785,0.8725,0.4657,-3.2346,-0.24604,0.48852,-0.83714,210.48,-0.95792,0.0091875,0.2869,210.23
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.14785,0.8725,0.4657,-72.613,-0.24604,0.48852,-0.83714,211.81,-0.95792,0.0091875,0.2869,205.44
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.12372,0.72067,0.68215,-49.094,0.065146,0.69184,-0.7191,130.45,-0.99018,-0.044529,-0.13254,274.4
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.12372,0.72067,0.68215,-52.059,0.065146,0.69184,-0.7191,130.58,-0.99018,-0.044529,-0.13254,270.2
> fitmap #23 inMap #21
Fit map cryosparc_P4_J169_class_04_00182_volume_sharp.mrc in map
cryosparc_P4_J169_class_02_00182_volume_sharp.mrc using 20956 points
correlation = 0.8996, correlation about mean = 0.4033, overlap = 1373
steps = 168, shift = 14.7, angle = 39.5 degrees
Position of cryosparc_P4_J169_class_04_00182_volume_sharp.mrc (#23) relative
to cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) coordinates:
Matrix rotation and translation
-0.99961182 0.01552465 -0.02313457 267.26750037
0.02397017 0.90245504 -0.43011668 70.06567251
0.01420050 -0.43050425 -0.90247684 305.57661651
Axis -0.01012464 -0.97530665 0.22062281
Axis point 131.76679627 0.00000000 162.02424501
Rotation angle (degrees) 178.90328205
Shift along axis -3.62433410
> select subtract #23
Nothing selected
> hide #!23 models
> hide #!21 models
> show #!23 models
> volume #23 level 0.1996
> hide #!23 models
> show #!22 models
> volume #22 level 0.2715
> hide #!22 models
> show #!21 models
> volume #21 level 0.2481
> hide #!21 models
> show #!20 models
> volume #20 level 0.198
> hide #!20 models
> show #!19 models
> volume #19 level 0.1357
> volume #19 level 0.1565
> color #9 #FCEDFF
> show #!9 models
> hide #!9 models
> color #19 #FCEDFF
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> hide #!19 models
> show #!20 models
> color #20 #FCEDFF
> hide #!20 models
> show #!21 models
> show #!20 models
> hide #!20 models
> color #21 #FCEDFF
> hide #!21 models
> show #!22 models
> show #!23 models
> hide #!22 models
> color #23 #FCEDFF
> color #22 #99BFE5
> show #!22 models
> hide #!23 models
> hide #!22 models
> show #!22 models
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> view P1
> save P4_J169_class_3_sharp.png supersample 3 transparentBackground true
> hide #!22 models
> show #!19 models
> save P4_J169_class_0_sharp.png supersample 3 transparentBackground true
> hide #!19 models
> show #!20 models
> save P4_J169_class_1_sharp.png supersample 3 transparentBackground true
> hide #!20 models
> show #!21 models
> save P4_J169_class_2_sharp.png supersample 3 transparentBackground true
> hide #!21 models
> show #!22 models
> show #!23 models
> hide #!22 models
> save P4_J169_class_4_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J176_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J176_002_volume_map_sharp.mrc as #24, grid size 80,80,80,
pixel 3.32, shown at level 1.05, step 1, values float32
> show #!22 models
> hide #!23 models
> select add #24
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.60544,-0.7944,-0.048687,168.77,-0.79404,-0.60707,0.031193,325.29,-0.054337,0.019774,-0.99833,244.32
> view matrix models
> #24,0.59955,-0.80023,-0.012763,166.07,-0.79939,-0.59954,0.03913,324.05,-0.038965,-0.013258,-0.99915,246.8
> view matrix models
> #24,0.55506,-0.74882,-0.36218,207.08,-0.8209,-0.56341,-0.093219,337.96,-0.13425,0.34906,-0.92744,201.93
> view matrix models
> #24,0.18767,0.98161,-0.034938,-17.516,0.95411,-0.19063,-0.23093,58.314,-0.23335,0.010004,-0.97234,267.28
> volume flip #24
Opened cryosparc_P4_J176_002_volume_map_sharp.mrc z flip as #25, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #24
> select add #25
2 models selected
> view matrix models
> #25,-0.63444,0.77032,-0.064025,129.07,-0.77136,-0.63629,-0.011971,326.31,-0.04996,0.041792,0.99788,-43.633
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.63444,0.77032,-0.064025,133.77,-0.77136,-0.63629,-0.011971,326.45,-0.04996,0.041792,0.99788,5.2846
> fitmap #25 inMap #22
Fit map cryosparc_P4_J176_002_volume_map_sharp.mrc z flip in map
CS_P4_J169_class_03_sharp_flip.mrc using 5115 points
correlation = 0.927, correlation about mean = 0.5943, overlap = 3935
steps = 92, shift = 11.4, angle = 9.34 degrees
Position of cryosparc_P4_J176_002_volume_map_sharp.mrc z flip (#25) relative
to CS_P4_J169_class_03_sharp_flip.mrc (#22) coordinates:
Matrix rotation and translation
-0.48979714 -0.86290735 -0.12445753 333.02911722
0.86312907 -0.50006428 0.07031310 74.16708713
-0.12291046 -0.07298376 0.98973047 29.10111268
Axis -0.08273609 -0.00089324 0.99657109
Axis point 146.24021491 133.58927656 0.00000000
Rotation angle (degrees) 120.00433179
Shift along axis 1.38155071
> select subtract #25
Nothing selected
> rename #25 CS_P4_J176_NU_sharp_flip id #24
> save CS_P4_J176_NU_sharp_flip.mrc #24
> hide #!22 models
> volume #24 level 1.757
> volume #24 level 1.364
> color #24 #99BFE5
> volume #24 level 1.6
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow.cxs"
> view P1
> save CS_P4_J176_NU_sharp.png supersample 3 transparentBackground true
> open "/Users/peiyuyu/Documents/Goethe University/19. Model Building/2. AcrF
> Project/1. Apo-form/LG-F_Apo/Map/cryosparc_P10_J41_007_volume_map_sharp.mrc"
Opened cryosparc_P10_J41_007_volume_map_sharp.mrc as #25, grid size
320,320,320, pixel 0.831, shown at level 0.123, step 2, values float32
> hide #!24 models
> show #!22 models
> hide #!22 models
> volume #25 level 0.2164
> save CS_P10_J41_NU_sharp_flip.mrc #25
> close #25
> show #!24 models
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260501_SA-F_B1_workflow1.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J255_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J255_002_volume_map_sharp.mrc as #25, grid size 80,80,80,
pixel 3.32, shown at level 0.649, step 1, values float32
> hide #!24 models
> volume flip #25
Opened cryosparc_P4_J255_002_volume_map_sharp.mrc z flip as #26, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #25
> rename CS_P4_J255_sharp_flip id #25
Missing or invalid "models" argument: invalid models specifier
> rename #26 CS_P4_J255_sharp_flip id #25
> save CS_P4_J255_sharp_flip.mrc #25
> show #!21 models
> hide #!21 models
> show #!24 models
> fitmap #25 inMap #24
Fit map CS_P4_J255_sharp_flip.mrc in map CS_P4_J176_NU_sharp_flip.mrc using
5116 points
correlation = 0.3392, correlation about mean = 0.06206, overlap = 2168
steps = 64, shift = 8.32, angle = 5.45 degrees
Position of CS_P4_J255_sharp_flip.mrc (#25) relative to
CS_P4_J176_NU_sharp_flip.mrc (#24) coordinates:
Matrix rotation and translation
-0.61720035 -0.75989860 -0.20400451 353.05950420
0.73150715 -0.64968488 0.20689815 96.93395715
-0.28976026 -0.02153315 0.95685700 43.12583281
Axis -0.15115555 0.05674554 0.98687990
Axis point 157.34041998 128.70985965 0.00000000
Rotation angle (degrees) 130.92072050
Shift along axis -5.30631665
> ui mousemode right "rotate selected models"
> select add #25
2 models selected
> view matrix models
> #25,-0.47042,-0.83357,-0.28961,363.38,0.84754,-0.51818,0.11478,76.044,-0.24575,-0.19146,0.95024,72.926
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.47042,-0.83357,-0.28961,355.09,0.84754,-0.51818,0.11478,66.81,-0.24575,-0.19146,0.95024,74.95
> view matrix models
> #25,-0.47042,-0.83357,-0.28961,355.15,0.84754,-0.51818,0.11478,66.803,-0.24575,-0.19146,0.95024,74.561
> fitmap #25 inMap #24
Fit map CS_P4_J255_sharp_flip.mrc in map CS_P4_J176_NU_sharp_flip.mrc using
5116 points
correlation = 0.8943, correlation about mean = 0.6059, overlap = 8709
steps = 84, shift = 8.95, angle = 14.5 degrees
Position of CS_P4_J255_sharp_flip.mrc (#25) relative to
CS_P4_J176_NU_sharp_flip.mrc (#24) coordinates:
Matrix rotation and translation
-0.48869161 0.86324945 -0.12641554 102.63693670
-0.86157381 -0.50031742 -0.08586638 328.42188396
-0.13737200 0.06695414 0.98825405 11.50507804
Axis 0.08825319 0.00632731 -0.99607798
Axis point 146.96136624 134.50878130 0.00000000
Rotation angle (degrees) 120.02497766
Shift along axis -0.32389146
> select subtract #25
Nothing selected
> save CS_P4_J255_sharp_flip.mrc #25
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J256_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J256_003_volume_map_sharp.mrc as #26, grid size 80,80,80,
pixel 3.32, shown at level 1.01, step 1, values float32
> hide #!25 models
> hide #!24 models
> select add #26
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.89385,-0.39986,0.20284,290.33,-0.34063,0.89978,0.2727,28.49,-0.29155,0.17466,-0.94047,242.77
> select subtract #26
Nothing selected
> show #!25 models
> fitmap #26 inMap #25
Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc in map
CS_P4_J255_sharp_flip.mrc using 5120 points
correlation = 0.5232, correlation about mean = 0.0553, overlap = 3214
steps = 120, shift = 25.3, angle = 15.3 degrees
Position of cryosparc_P4_J256_003_volume_map_sharp.mrc (#26) relative to
CS_P4_J255_sharp_flip.mrc (#25) coordinates:
Matrix rotation and translation
-0.15531756 0.84438274 0.51273214 -19.64184672
0.98713928 0.15254692 0.04780678 -29.86548711
-0.03784849 0.51356326 -0.85721658 167.46829582
Axis 0.63355180 0.74893504 0.19418658
Axis point 24.16142457 0.00000000 89.91884511
Rotation angle (degrees) 158.43381860
Shift along axis -2.29134077
> select add #26
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.87857,-0.47692,-0.025855,314.85,-0.44818,0.80449,0.38978,38.161,-0.16509,0.35404,-0.92054,233.61
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.93629,-0.25688,0.23952,260.92,-0.23661,0.96532,0.11035,19.606,-0.25956,0.046645,-0.9646,294.56
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.93629,-0.25688,0.23952,186.31,-0.23661,0.96532,0.11035,26.555,-0.25956,0.046645,-0.9646,285.53
> select subtract #26
Nothing selected
> volume flip #26
Opened cryosparc_P4_J256_003_volume_map_sharp.mrc z flip as #27, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #26
> select add #27
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #27,-0.91261,-0.40844,0.017647,236.5,0.22697,-0.47029,0.85283,55.691,-0.34003,0.78231,0.5219,-22.328
> view matrix models
> #27,-0.9144,-0.40478,0.0045882,238.13,0.22235,-0.49276,0.84128,61.136,-0.33827,0.77029,0.54058,-23.608
> view matrix models
> #27,-0.50015,0.79795,-0.33634,63.369,-0.80597,-0.57099,-0.15615,357.35,-0.31664,0.19298,0.92871,-2.4372
> ui mousemode right "translate selected models"
> view matrix models
> #27,-0.50015,0.79795,-0.33634,139.66,-0.80597,-0.57099,-0.15615,346.55,-0.31664,0.19298,0.92871,33.757
> fitmap #27 inMap #25
Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc z flip in map
CS_P4_J255_sharp_flip.mrc using 5120 points
correlation = 0.5523, correlation about mean = 0.08213, overlap = 3668
steps = 72, shift = 2.85, angle = 5.49 degrees
Position of cryosparc_P4_J256_003_volume_map_sharp.mrc z flip (#27) relative
to CS_P4_J255_sharp_flip.mrc (#25) coordinates:
Matrix rotation and translation
-0.50078193 -0.83716343 -0.21994286 353.70374510
0.81104417 -0.54259583 0.21862553 68.19134780
-0.30236538 -0.06889966 0.95069870 54.62167416
Axis -0.17164375 0.04920372 0.98392958
Axis point 162.79794553 129.91438640 0.00000000
Rotation angle (degrees) 123.11624986
Shift along axis -3.61188964
> view matrix models
> #27,-0.56613,0.75777,-0.32448,155.66,-0.74832,-0.63753,-0.18323,351.66,-0.34571,0.13908,0.92798,47.028
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.96274,0.27031,-0.0085132,-30.789,-0.27044,0.96237,-0.026732,40.459,0.00096683,0.028039,0.99961,4.8234
> fitmap #27 inMap #25
Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc z flip in map
CS_P4_J255_sharp_flip.mrc using 5120 points
correlation = 0.9111, correlation about mean = 0.5876, overlap = 9195
steps = 60, shift = 4.49, angle = 4.9 degrees
Position of cryosparc_P4_J256_003_volume_map_sharp.mrc z flip (#27) relative
to CS_P4_J255_sharp_flip.mrc (#25) coordinates:
Matrix rotation and translation
-0.48877401 0.86149397 -0.13757950 104.57166396
-0.86119668 -0.50165763 -0.08173068 327.97179743
-0.13942829 0.07853517 0.98711295 10.19538079
Axis 0.09263223 0.00106859 -0.99569982
Axis point 147.63593381 133.73777093 0.00000000
Rotation angle (degrees) 120.10984192
Shift along axis -0.11436514
> select subtract #27
Nothing selected
> hide #!25 models
> rename #27 CS_P4_J256_sharp_flip id #26
> save CS_P4_J256_sharp_flip.mrc #26
> show #!25 models
> hide #!25 models
> hide #!26 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J257_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J257_002_volume_map_sharp.mrc as #27, grid size 80,80,80,
pixel 3.32, shown at level 0.915, step 1, values float32
> select add #27
2 models selected
> show #!26 models
> view matrix models
> #27,0.43348,0.88304,0.17982,-64.533,0.89699,-0.44198,0.0081618,72.887,0.086685,0.15776,-0.98367,205.49
> hide #!26 models
> select subtract #27
Nothing selected
> volume flip #27
Opened cryosparc_P4_J257_002_volume_map_sharp.mrc z flip as #28, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #27
> select add #28
2 models selected
> show #!26 models
> view matrix models
> #28,0.0384,0.0015757,0.99926,-5.8546,0.92609,-0.37568,-0.034996,65.933,0.37535,0.92675,-0.015886,-77.078
> view matrix models
> #28,0.75378,0.65514,-0.051086,-44.642,-0.54582,0.58092,-0.60384,218.55,-0.36592,0.48304,0.79547,-29.499
> view matrix models
> #28,0.93053,0.32568,-0.16747,-7.3436,-0.34314,0.93516,-0.087963,68.823,0.12796,0.13932,0.98195,-76.969
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.93053,0.32568,-0.16747,-12.031,-0.34314,0.93516,-0.087963,69.72,0.12796,0.13932,0.98195,-23.264
> select subtract #28
Nothing selected
> fitmap #28 inMap #26
Fit map cryosparc_P4_J257_002_volume_map_sharp.mrc z flip in map
CS_P4_J256_sharp_flip.mrc using 5113 points
correlation = 0.961, correlation about mean = 0.8355, overlap = 1.813e+04
steps = 76, shift = 3.44, angle = 10.7 degrees
Position of cryosparc_P4_J257_002_volume_map_sharp.mrc z flip (#28) relative
to CS_P4_J256_sharp_flip.mrc (#26) coordinates:
Matrix rotation and translation
0.99983973 0.00266136 0.01770477 -3.60430289
-0.00275366 0.99998275 0.00519130 -0.72993632
-0.01769065 -0.00523922 0.99982979 3.00234542
Axis -0.27967225 0.94905354 -0.14519233
Axis point 166.73187411 0.00000000 206.99324341
Rotation angle (degrees) 1.06849905
Shift along axis -0.12064266
> rename #28 CS_P4_J257_sharp_flip id #27
> save CS_P4_J257_sharp_flip.mrc #27
> hide #!26 models
> hide #!27 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J258_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J258_002_volume_map_sharp.mrc as #28, grid size 80,80,80,
pixel 3.32, shown at level 0.533, step 1, values float32
> select add #28
2 models selected
> show #!27 models
> view matrix models #28,1,0,0,2.9293,0,1,0,12.799,0,0,1,30.196
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.94564,-0.32466,0.018849,316.84,-0.32175,0.94244,0.090998,54.708,-0.047307,0.079987,-0.99567,265.03
> select up
56 models selected
> select up
56 models selected
> select down
2 models selected
> select down
2 models selected
> select subtract #28
Nothing selected
> hide #!27 models
> volume flip #28
Opened cryosparc_P4_J258_002_volume_map_sharp.mrc z flip as #29, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #28
> select add #29
2 models selected
> view matrix models
> #29,0.95822,0.27409,-0.081793,-16.892,-0.27702,0.96049,-0.026814,62.796,0.071212,0.048352,0.99629,-31.428
> show #!27 models
> select subtract #29
Nothing selected
> fitmap #29 inMap #27
Fit map cryosparc_P4_J258_002_volume_map_sharp.mrc z flip in map
CS_P4_J257_sharp_flip.mrc using 5117 points
correlation = 0.4043, correlation about mean = 0.1105, overlap = 1145
steps = 104, shift = 9.56, angle = 9.45 degrees
Position of cryosparc_P4_J258_002_volume_map_sharp.mrc z flip (#29) relative
to CS_P4_J257_sharp_flip.mrc (#27) coordinates:
Matrix rotation and translation
0.98218261 0.18784329 -0.00567361 -27.82492616
-0.18685004 0.97932905 0.07747035 28.59524537
0.02010861 -0.07502992 0.99697851 -24.36927466
Axis -0.37621012 -0.06360338 -0.92434872
Axis point 152.56947582 100.16313614 0.00000000
Rotation angle (degrees) 11.69370116
Shift along axis 31.17497259
> select add #29
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.91472,0.40193,-0.041674,-52.044,-0.39883,0.91458,0.066882,60.074,0.064997,-0.044558,0.99689,0.70588
> view matrix models
> #29,0.91472,0.40193,-0.041674,-39.705,-0.39883,0.91458,0.066882,54.066,0.064997,-0.044558,0.99689,6.2725
> fitmap #29 inMap #27
Fit map cryosparc_P4_J258_002_volume_map_sharp.mrc z flip in map
CS_P4_J257_sharp_flip.mrc using 5117 points
correlation = 0.8335, correlation about mean = 0.5457, overlap = 5135
steps = 64, shift = 1.52, angle = 12.1 degrees
Position of cryosparc_P4_J258_002_volume_map_sharp.mrc z flip (#29) relative
to CS_P4_J257_sharp_flip.mrc (#27) coordinates:
Matrix rotation and translation
0.99996433 -0.00752131 -0.00383843 1.74823892
0.00752090 0.99997170 -0.00012121 -0.88867123
0.00383923 0.00009234 0.99999262 -0.68815928
Axis 0.01264381 -0.45457780 0.89061729
Axis point 130.32470586 232.13443622 0.00000000
Rotation angle (degrees) 0.48385831
Shift along axis -0.18681194
> select subtract #29
Nothing selected
> rename #29 CS_P4_J258_sharp_flip id #28
> save CS_P4_J258_sharp_flip.mrc #28
> hide #!27 models
> hide #!28 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J259_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J259_002_volume_map_sharp.mrc as #29, grid size 80,80,80,
pixel 3.32, shown at level 0.567, step 1, values float32
> select add #29
2 models selected
> show #!28 models
> view matrix models #29,1,0,0,-4.0284,0,1,0,3.9973,0,0,1,26.374
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.37373,0.91624,0.14434,-63.019,0.92743,-0.36674,-0.073343,74.867,-0.014266,0.16128,-0.98681,258.72
> view matrix models
> #29,0.2129,0.93735,0.27578,-60.698,0.97539,-0.1873,-0.11636,49.108,-0.057419,0.29377,-0.95415,242.23
> hide #!28 models
> select subtract #29
Nothing selected
> volume flip #29
Opened cryosparc_P4_J259_002_volume_map_sharp.mrc z flip as #30, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #29
> select add #30
2 models selected
> show #!28 models
> view matrix models
> #30,0.90176,0.31537,-0.29559,8.3185,-0.32745,0.94483,0.0091223,54.046,0.28216,0.088565,0.95527,-34.506
> select subtract #30
Nothing selected
> fitmap #30 inMap #28
Fit map cryosparc_P4_J259_002_volume_map_sharp.mrc z flip in map
CS_P4_J258_sharp_flip.mrc using 5112 points
correlation = 0.9666, correlation about mean = 0.6628, overlap = 3020
steps = 80, shift = 5.99, angle = 15.1 degrees
Position of cryosparc_P4_J259_002_volume_map_sharp.mrc z flip (#30) relative
to CS_P4_J258_sharp_flip.mrc (#28) coordinates:
Matrix rotation and translation
0.99996699 0.00262374 -0.00768921 0.94371527
-0.00261765 0.99999625 0.00080251 0.08556771
0.00769129 -0.00078235 0.99997011 -0.47262490
Axis -0.09707497 -0.94207663 -0.32104217
Axis point 62.77947672 0.00000000 122.20423531
Rotation angle (degrees) 0.46771540
Shift along axis -0.02048995
> rename #30 CS_P4_J259_sharp_flip id #29
> save CS_P4_J259_sharp_flip.mrc #29
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow.cxs"
> hide #!29 models
> hide #!28 models
> show #!25 models
> color #25 #FCEDFF
> hide #!25 models
> show #!28 models
> color #28 #FCEDFF
> hide #!28 models
> show #!29 models
> color #29 #FCEDFF
> hide #!29 models
> show #!29 models
> show #!26 models
> hide #!29 models
> color #26 #99BFE5
> hide #!26 models
> show #!27 models
> color #27 #99BFE5
> view P1
> hide #!27 models
> show #!25 models
> ui mousemode right "translate selected models"
> ui mousemode right translate
> view P1
> save CS_P4_J255_NU_sharp.png supersample 3 transparentBackground true
> hide #!25 models
> show #!26 models
> volume #26 level 1.012
> save CS_P4_J256_NU_sharp.png supersample 3 transparentBackground true
> hide #!26 models
> show #!27 models
> save CS_P4_J257_NU_sharp.png supersample 3 transparentBackground true
> hide #!27 models
> show #!28 models
> save CS_P4_J258_NU_sharp.png supersample 3 transparentBackground true
> hide #!28 models
> show #!29 models
> save CS_P4_J259_NU_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #30, grid size
320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J267_008_volume_map_sharp.mrc"
Opened cryosparc_P4_J267_008_volume_map_sharp.mrc as #31, grid size
320,320,320, pixel 0.831, shown at level 0.0747, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J277_008_volume_map_sharp.mrc"
Opened cryosparc_P4_J277_008_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0762, step 2, values float32
> hide #!29 models
> hide #!30 models
> hide #!31 models
> show #!31 models
> hide #!32 models
> show #!30 models
> close #30
> show #!27 models
> select add #31
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #31,-0.90396,0.26529,0.33537,196.37,0.29187,0.95597,0.030503,-41.724,-0.31251,0.12546,-0.94159,315.51
> hide #!27 models
> view matrix models
> #31,-0.95736,-0.095902,0.27253,266.49,-0.06692,0.99125,0.11374,-5.5307,-0.28105,0.090649,-0.9554,317.94
> show #!29 models
> hide #!29 models
> select subtract #31
Nothing selected
> close #32
> volume flip #31
Opened cryosparc_P4_J267_008_volume_map_sharp.mrc z flip as #30, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> close #30
> show #!31 models
> select add #31
2 models selected
> show #!27 models
> ui mousemode right "translate selected models"
> view matrix models
> #31,-0.95736,-0.095902,0.27253,258.1,-0.06692,0.99125,0.11374,14.401,-0.28105,0.090649,-0.9554,295.97
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.57983,0.79903,0.15922,-85.975,0.81408,-0.57604,-0.073785,139.64,0.032763,0.1724,-0.98448,241.38
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.57983,0.79903,0.15922,-74.26,0.81408,-0.57604,-0.073785,114.14,0.032763,0.1724,-0.98448,243.66
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.38773,0.91358,0.12259,-56.869,0.92165,-0.3821,-0.067497,68.753,-0.014823,0.13915,-0.99016,256.48
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.38773,0.91358,0.12259,-59.17,0.92165,-0.3821,-0.067497,73.776,-0.014823,0.13915,-0.99016,255.81
> fitmap #31 inMap #27
Fit map cryosparc_P4_J267_008_volume_map_sharp.mrc in map
CS_P4_J257_sharp_flip.mrc using 40948 points
correlation = 0.4368, correlation about mean = 0.04808, overlap = 2838
steps = 84, shift = 6.03, angle = 16 degrees
Position of cryosparc_P4_J267_008_volume_map_sharp.mrc (#31) relative to
CS_P4_J257_sharp_flip.mrc (#27) coordinates:
Matrix rotation and translation
-0.09805932 0.98945486 0.10659935 2.84911711
0.99008140 0.10782511 -0.09006967 -2.59568012
-0.10061396 0.09670986 -0.99021412 262.50076525
Axis 0.66953234 0.74277951 0.00224590
Axis point 14.97851108 -0.00000000 131.13786872
Rotation angle (degrees) 171.98194915
Shift along axis 0.56910865
> select subtract #31
Nothing selected
> hide #!31 models
> hide #!27 models
> show #!31 models
> close #31
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J267_008_volume_map_sharp.mrc"
Opened cryosparc_P4_J267_008_volume_map_sharp.mrc as #30, grid size
320,320,320, pixel 0.831, shown at level 0.0747, step 2, values float32
> select add #30
2 models selected
> show #!27 models
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.59059,-0.80637,-0.031153,183.8,-0.80688,-0.59066,-0.008015,354.56,-0.011937,0.02987,-0.99948,293.1
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.59059,-0.80637,-0.031153,187.84,-0.80688,-0.59066,-0.008015,342.67,-0.011937,0.02987,-0.99948,267.57
> hide #!27 models
> show #!27 models
> hide #!30 models
> hide #!27 models
> show #!30 models
> volume flip #30
Opened cryosparc_P4_J267_008_volume_map_sharp.mrc z flip as #31, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> select subtract #30
Nothing selected
> close #30
> select add #31
2 models selected
> show #!27 models
> view matrix models
> #31,0.59059,-0.80637,-0.031153,181.08,-0.80688,-0.59066,-0.008015,342.68,-0.011937,0.02987,-0.99948,285.6
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.49825,-0.85813,0.12394,182.63,-0.032454,0.12438,0.9917,19.314,-0.86642,-0.49814,0.034125,354.11
> view matrix models
> #31,-0.47795,-0.87619,-0.061991,343.39,0.85267,-0.47976,0.20686,70.492,-0.21099,0.046011,0.9764,77.316
> ui mousemode right "translate selected models"
> view matrix models
> #31,-0.47795,-0.87619,-0.061991,322.39,0.85267,-0.47976,0.20686,71.691,-0.21099,0.046011,0.9764,36.515
> view matrix models
> #31,-0.47795,-0.87619,-0.061991,329.78,0.85267,-0.47976,0.20686,58.248,-0.21099,0.046011,0.9764,36.244
> fitmap #31 inMap #27
Fit map cryosparc_P4_J267_008_volume_map_sharp.mrc z flip in map
CS_P4_J257_sharp_flip.mrc using 327854 points
correlation = 0.6967, correlation about mean = 0.2684, overlap = 4.49e+04
steps = 92, shift = 8.63, angle = 16.2 degrees
Position of cryosparc_P4_J267_008_volume_map_sharp.mrc z flip (#31) relative
to CS_P4_J257_sharp_flip.mrc (#27) coordinates:
Matrix rotation and translation
-0.48810574 -0.85845883 -0.15748400 338.09346066
0.86132304 -0.50293557 0.07196129 74.97027819
-0.14098011 -0.10051988 0.98489611 32.48936744
Axis -0.09978729 -0.00954816 0.99496298
Axis point 149.01931346 135.27108975 0.00000000
Rotation angle (degrees) 120.20349080
Shift along axis -2.12754240
> select subtract #31
Nothing selected
> volume #27 level 1.164
> volume #31 level 0.1055
> hide #!27 models
> volume #31 level 0.1343
> color #31 #99BFE5
> rename #31 CS_P4_J267_sharp_flip id #30
> save CS_P4_J267_sharp_flip.mrc #30
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J277_008_volume_map_sharp.mrc"
Opened cryosparc_P4_J277_008_volume_map_sharp.mrc as #31, grid size
320,320,320, pixel 0.831, shown at level 0.0762, step 2, values float32
> hide #!30 models
> select add #31
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.50169,-0.77701,0.38022,112.38,-0.8444,-0.53533,0.020189,301.01,0.18786,-0.33119,-0.92467,273.22
> view matrix models
> #31,0.77218,-0.62718,0.10187,94.664,-0.63536,-0.764,0.11236,288.83,0.0073633,-0.15149,-0.98843,283.82
> volume flip #31
Opened cryosparc_P4_J277_008_volume_map_sharp.mrc z flip as #32, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> close #31
> select add #32
2 models selected
> show #!30 models
> view matrix models
> #32,0.90608,0.27127,-0.3247,15.596,-0.28323,0.95899,0.010829,28.44,0.31432,0.082155,0.94575,-47.16
> view matrix models
> #32,0.99239,-0.018676,-0.12173,15.559,0.019459,0.9998,0.0052468,-15.401,0.1216,-0.0075755,0.99255,-16.612
> ui mousemode right "translate selected models"
> view matrix models
> #32,0.99239,-0.018676,-0.12173,21.14,0.019459,0.9998,0.0052468,-2.6957,0.1216,-0.0075755,0.99255,-9.4459
> fitmap #32 inMap #30
Fit map cryosparc_P4_J277_008_volume_map_sharp.mrc z flip in map
CS_P4_J267_sharp_flip.mrc using 327711 points
correlation = 0.7196, correlation about mean = 0.3385, overlap = 5671
steps = 204, shift = 3.68, angle = 13.7 degrees
Position of cryosparc_P4_J277_008_volume_map_sharp.mrc z flip (#32) relative
to CS_P4_J267_sharp_flip.mrc (#30) coordinates:
Matrix rotation and translation
-0.48144357 0.86501463 -0.14128627 103.86408789
-0.86432037 -0.49531179 -0.08727288 328.52215562
-0.14547307 0.08009963 0.98611442 10.75546195
Axis 0.09633390 0.00240978 -0.99534616
Axis point 148.32654443 133.96556119 0.00000000
Rotation angle (degrees) 119.69088439
Shift along axis 0.09189113
> select subtract #32
Nothing selected
> volume #32 level 0.1306
> hide #!30 models
> volume #32 level 0.1432
> color #32 #99BFE5
> rename #32 CS_P4_J277_sharp_flip id #31
> save CS_P4_J277_sharp_flip.mrc #31
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32
> hide #!31 models
> select add #32
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #32,0.30706,0.95043,0.049005,-33.318,0.9497,-0.30268,-0.080397,47.411,-0.061579,0.071226,-0.99556,261.24
> volume flip #32
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #33, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> show #!31 models
> show #!32 models
> view matrix models
> #32,0.19586,0.82677,-0.52734,72.951,0.95192,-0.28947,-0.10029,48.053,-0.23556,-0.48235,-0.84371,334.74
> view matrix models
> #32,0.038463,0.98737,0.15371,-15.568,0.97818,-0.0057722,-0.20769,22.74,-0.20418,0.15835,-0.96604,265.55
> close #32
> select add #33
2 models selected
> view matrix models
> #33,-0.36526,-0.91739,-0.15805,324.89,0.9276,-0.34439,-0.14472,64.223,0.078335,-0.19947,0.97677,17.619
> view matrix models
> #33,-0.3296,-0.92737,-0.17708,323.89,0.91639,-0.35937,0.17633,25.386,-0.22716,-0.10416,0.96827,47.503
> select subtract #33
Nothing selected
> fitmap #33 inMap #31
Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map
CS_P4_J277_sharp_flip.mrc using 327344 points
correlation = 0.3754, correlation about mean = 0.04431, overlap = 1099
steps = 64, shift = 4.4, angle = 1.24 degrees
Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative
to CS_P4_J277_sharp_flip.mrc (#31) coordinates:
Matrix rotation and translation
-0.52307807 -0.83656982 -0.16291178 338.77635518
0.81824450 -0.54640858 0.17864376 66.60900444
-0.23846438 -0.03985703 0.97033300 35.38091339
Axis -0.13076939 0.04521708 0.99038113
Axis point 153.51682890 124.48577590 0.00000000
Rotation angle (degrees) 123.33798629
Shift along axis -6.24912375
> volume #33 level 0.05666
> select add #33
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #33,-0.32295,-0.92807,-0.18543,326.53,0.9135,-0.3569,0.19529,26.322,-0.24742,-0.10632,0.96306,60.406
> fitmap #33 inMap #31
Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map
CS_P4_J277_sharp_flip.mrc using 194771 points
correlation = 0.7316, correlation about mean = 0.2783, overlap = 2429
steps = 104, shift = 3.72, angle = 6.69 degrees
Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative
to CS_P4_J277_sharp_flip.mrc (#31) coordinates:
Matrix rotation and translation
-0.48329817 -0.86312458 -0.14641999 335.54076959
0.86340511 -0.49758655 0.08330200 72.08568886
-0.14475663 -0.08616006 0.98570885 33.43360614
Axis -0.09768239 -0.00095880 0.99521718
Axis point 148.43445219 133.71191357 0.00000000
Rotation angle (degrees) 119.84054702
Shift along axis 0.42815717
> select subtract #33
Nothing selected
> select add #33
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #33,-0.6364,0.75107,-0.17577,140.89,-0.74512,-0.6575,-0.11171,345.32,-0.19948,0.059876,0.97807,29.849
> ui mousemode right "translate selected models"
> view matrix models
> #33,-0.6364,0.75107,-0.17577,136.82,-0.74512,-0.6575,-0.11171,338.86,-0.19948,0.059876,0.97807,29.687
> ui mousemode right "rotate selected models"
> view matrix models
> #33,-0.73358,0.64738,-0.20678,168.84,-0.63708,-0.76101,-0.12246,339.46,-0.23664,0.041901,0.97069,38.344
> fitmap #33 inMap #31
Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map
CS_P4_J277_sharp_flip.mrc using 194771 points
correlation = 0.4346, correlation about mean = 0.05784, overlap = 1046
steps = 96, shift = 4.05, angle = 4.16 degrees
Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative
to CS_P4_J277_sharp_flip.mrc (#31) coordinates:
Matrix rotation and translation
-0.58502424 0.80932802 -0.05229508 107.72395607
-0.80221021 -0.58694418 -0.10934029 332.49911712
-0.11918646 -0.02201508 0.99262777 22.68232922
Axis 0.05406170 0.04141143 -0.99767852
Axis point 139.16943260 139.24984383 0.00000000
Rotation angle (degrees) 126.13361686
Shift along axis -3.03667024
> ui mousemode right "translate selected models"
> view matrix models
> #33,-0.7311,0.66788,-0.13939,159.58,-0.65889,-0.74418,-0.10984,339.55,-0.17709,0.011538,0.98413,33.11
> fitmap #33 inMap #31
Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map
CS_P4_J277_sharp_flip.mrc using 194771 points
correlation = 0.7261, correlation about mean = 0.2429, overlap = 2435
steps = 148, shift = 3.57, angle = 8.91 degrees
Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative
to CS_P4_J277_sharp_flip.mrc (#31) coordinates:
Matrix rotation and translation
-0.47691102 0.86730315 -0.14262219 103.16958211
-0.86637561 -0.49120809 -0.09004393 328.47939238
-0.14815256 0.08062145 0.98567285 11.48812128
Axis 0.09796714 0.00317460 -0.99518459
Axis point 148.54824739 133.97305983 0.00000000
Rotation angle (degrees) 119.42100612
Shift along axis -0.28278057
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.98687,0.16137,0.0076046,-28.356,-0.15803,0.97406,-0.16197,41.243,-0.033544,0.15864,0.98677,-7.5792
> ui mousemode right "translate selected models"
> view matrix models
> #33,0.98687,0.16137,0.0076046,-22.398,-0.15803,0.97406,-0.16197,51.235,-0.033544,0.15864,0.98677,-4.7399
> fitmap #33 inMap #31
Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map
CS_P4_J277_sharp_flip.mrc using 194771 points
correlation = 0.9896, correlation about mean = 0.9159, overlap = 4214
steps = 120, shift = 4.17, angle = 9.65 degrees
Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative
to CS_P4_J277_sharp_flip.mrc (#31) coordinates:
Matrix rotation and translation
0.99997973 -0.00439362 0.00460748 -0.02530815
0.00439161 0.99999024 0.00044636 -0.51759472
-0.00460939 -0.00042611 0.99998927 1.01725436
Axis -0.06835965 0.72216012 0.68833983
Axis point 171.68283436 0.00000000 1.37920014
Rotation angle (degrees) 0.36563312
Shift along axis 0.32816049
> select subtract #33
Nothing selected
> hide #!31 models
> show #!31 models
> hide #!31 models
> volume #33 level 0.06481
> color #33 #99BFE5
> view P1
> rename #33 CS_P4_J285_sharp_flip id #32
> save CS_P4_J285_sharp_flip.mrc #32
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow.cxs"
> save CS_P4_J285_NU_sharp.png supersample 3 transparentBackground true
> hide #!32 models
> show #!31 models
> save CS_P4_J277_NU_sharp.png supersample 3 transparentBackground true
> hide #!31 models
> show #!30 models
> save CS_P4_J267_NU_sharp.png supersample 3 transparentBackground true
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32
> select add #33
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.77382,-0.58736,0.23709,68.017,-0.6199,-0.77915,0.092993,287.71,0.13011,-0.21893,-0.96703,293.89
> volume flip sel
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #34, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> select subtract #33
Nothing selected
> select add #34
2 models selected
> view matrix models
> #34,0.96024,0.18105,-0.2125,4.9844,-0.18441,0.98284,0.0040821,22.146,0.20959,0.035266,0.97715,4.1522
> volume #34 level 0.06153
> ui mousemode right "translate selected models"
> view matrix models
> #34,0.96024,0.18105,-0.2125,5.3992,-0.18441,0.98284,0.0040821,24.944,0.20959,0.035266,0.97715,-19.851
> fitmap #34 inMap #30
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
CS_P4_J267_sharp_flip.mrc using 179913 points
correlation = 0.7668, correlation about mean = 0.2691, overlap = 2384
steps = 132, shift = 4.76, angle = 10.2 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative
to CS_P4_J267_sharp_flip.mrc (#30) coordinates:
Matrix rotation and translation
-0.47859383 0.86460690 -0.15297990 105.65226772
-0.86128787 -0.49615211 -0.10961884 331.90892973
-0.17067851 0.07929683 0.98213077 14.98614385
Axis 0.10880400 0.01019333 -0.99401096
Axis point 150.51207819 135.19673705 0.00000000
Rotation angle (degrees) 119.75601097
Shift along axis -0.01774616
> select subtract #34
Nothing selected
> select add #34
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #34,-0.29858,-0.92833,-0.22151,340.08,0.93935,-0.32688,0.10377,36.917,-0.16874,-0.17709,0.96962,60.484
> fitmap #34 inMap #30
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
CS_P4_J267_sharp_flip.mrc using 179913 points
correlation = 0.4184, correlation about mean = 0.03499, overlap = 815.8
steps = 72, shift = 3.19, angle = 2.56 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative
to CS_P4_J267_sharp_flip.mrc (#30) coordinates:
Matrix rotation and translation
0.99975679 -0.00914856 -0.02006678 -0.29483780
0.00937915 0.99989072 0.01142689 -12.23865962
0.01996005 -0.01161232 0.99973334 -0.12571505
Axis -0.46299067 -0.80436995 0.37232865
Axis point 194.44052306 0.00000000 212.15518455
Rotation angle (degrees) 1.42571524
Shift along axis 9.93410983
> ui mousemode right "translate selected models"
> view matrix models
> #34,-0.29149,-0.93644,-0.19523,323.34,0.9479,-0.31019,0.07257,35.755,-0.12852,-0.16391,0.97807,48.671
> fitmap #34 inMap #30
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
CS_P4_J267_sharp_flip.mrc using 179913 points
correlation = 0.9696, correlation about mean = 0.7683, overlap = 3705
steps = 76, shift = 2.39, angle = 2.68 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative
to CS_P4_J267_sharp_flip.mrc (#30) coordinates:
Matrix rotation and translation
0.99970034 -0.00006024 0.02447927 -4.11138943
0.00004629 0.99999984 0.00057062 0.05899118
-0.02447930 -0.00056932 0.99970018 3.40337319
Axis -0.02327752 0.99972667 0.00217546
Axis point 136.94050248 0.00000000 169.47617625
Rotation angle (degrees) 1.40308329
Shift along axis 0.16208189
> select subtract #34
Nothing selected
> hide #!30 models
> show #!32 models
> hide #!31 models
> volume #34 level 0.06805
> hide #!32 models
> view P1
> close #33
> rename #34 CS_P4_J282_sharp_flip id #33
> save CS_P4_J282_sharp_flip.mrc #33
> view P1
> save CS_P4_J282_NU_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow1.cxs"
> color #33 #99BFE5
> save CS_P4_J282_NU_sharp1.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow1.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J287_map_locres.mrc"
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 9.77, step 2, values float32
> rename #34 cryosparc_P4_J287_map_locres_forJ282
> select add #34
2 models selected
> view matrix models #34,1,0,0,-1.0935,0,1,0,0.90366,0,0,1,6.3532
> ui mousemode right "rotate selected models"
> view matrix models
> #34,0.41458,0.88648,0.20563,-71.892,0.90978,-0.4089,-0.07146,80.866,0.020734,0.2167,-0.97602,247.42
> view matrix models
> #34,0.40248,0.89866,0.17442,-67.589,0.91533,-0.39227,-0.091056,80.514,-0.013407,0.1963,-0.98045,255.56
> view matrix models
> #34,0.3547,0.92587,0.13022,-58.659,0.93218,-0.33944,-0.12576,75.687,-0.072238,0.166,-0.98348,268.27
> fitmap #34 inMap #33
Fit map cryosparc_P4_J287_map_locres_forJ282 in map CS_P4_J282_sharp_flip.mrc
using 40893 points
correlation = 0.2997, correlation about mean = 0.02148, overlap = 2955
steps = 140, shift = 9.61, angle = 2.61 degrees
Position of cryosparc_P4_J287_map_locres_forJ282 (#34) relative to
CS_P4_J282_sharp_flip.mrc (#33) coordinates:
Matrix rotation and translation
0.77162333 -0.63598985 0.01069393 118.29154644
-0.63440309 -0.76826072 0.08548800 317.77796206
-0.04615378 -0.07274879 -0.99628182 298.10083492
Axis -0.94106809 0.33808548 0.00943679
Axis point 0.00000000 186.80747823 142.52542945
Rotation angle (degrees) 175.17728056
Shift along axis -1.07117046
> volume #34 level 6.762
> view matrix models
> #34,0.42433,0.90126,0.087581,-65.663,0.89997,-0.40908,-0.15069,88.731,-0.099987,0.14276,-0.98469,281
> ui mousemode right "translate selected models"
> view matrix models
> #34,0.42433,0.90126,0.087581,-62.736,0.89997,-0.40908,-0.15069,86.303,-0.099987,0.14276,-0.98469,272.65
> view matrix models
> #34,0.42433,0.90126,0.087581,-62.591,0.89997,-0.40908,-0.15069,86.167,-0.099987,0.14276,-0.98469,272.2
> volume #34 level 6.762
> volume #34 level 6.47
> ui tool show "Surface Color"
> color sample #33.1 map #34 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> select subtract #34
Nothing selected
> hide #!34 models
> key red-white-blue :0.0 :20.4 :40.8 showTool true
> ui mousemode right "color key"
> key red-white-blue :0.0 :20.4 :40.8 white:
> key red:0.0 white:20.4 blue:40.8 white: white:
> key red:0.0 white:20.4 blue:40.8 white:
> key red-white-blue :0.0 :20.4 :40.8
> key red-white-blue :0 :2 :4 showTool true
> ui mousemode right "color key"
> key red-white-blue :0 :2 :4 white:
> key red:0 white:2 blue:4 white: white:
> color single #33.1
> color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> key red-white-blue :0 :2 :4 showTool true
> ui mousemode right "color key"
> key red-white-blue :0 :2 :4 showTool true
> key red-white-blue :0 :2 :4 white:
> key red:0 white:2 blue:4 white: white:
> key red:0 white:2 blue:4 white: white:0
> key red:0 white:2 blue:4 white:1 white:0
> key red:0 white:2 blue:2 white:1 white:0
> key red:0 white:3 blue:2 white:1 white:0
> key red:4 white:3 blue:2 white:1 white:0
> key gnbu :4 :3 :2 :1 :0
> key esmfold :4 :3 :2 :1 :0
> key dark2-5 :4 :3 :2 :1 :0
> key pastel1-5 :4 :3 :2 :1 :0
> key blues :4 :3 :2 :1 :0
> key accent-5 :4 :3 :2 :1 :0
> color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> color sample #33.1 map #34 palette 0,#0000ff:2,#7f7fff:4,#ffffff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> key blue:0 #7f7fff:2 white:4 showTool true
> ui mousemode right "color key"
> key blue:0 #7f7fff:2 white:4 showTool true
> key blue:0 #7f7fff:2 white:4 white:
> key blue:0 #7f7fff:2 white:4 white: white:
> color sample #33.1 map #34 palette
> 0,#0000ff:1,#7f7fff:2,#ffffff:3,#ff7f7f:4,#ff0000 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> key blue:0 #7f7fff:1 white:2 #ff7f7f:3 red:4 showTool true
> ui mousemode right "color key"
> color sample #33.1 map #34 palette
> 0,#0000ff:1,#7f7fff:2,#ffffff:3,#ff7f7f:4,#ff0000 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> color sample #33.1 map #34 palette
> 0,#ff0000:1,#ff7f7f:2,#ffffff:3,#7f7fff:4,#0000ff outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> color sample #33.1 map #34 palette
> 0,#ff0000:2,#ff7f7f:4,#ffffff:5,#7f7fff:8,#0000ff outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.349, maximum 40.76
> volume #33 level 0.08574
> key red:0 #ff7f7f:2 white:4 #7f7fff:5 blue:8 showTool true
> key red:0 #ff7f7f:2 white:4 #7f7fff:6 blue:8 showTool true
> color sample #33.1 map #34 palette
> 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff7f7f:8,#ff0000 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> color sample #33.1 map #34 palette
> 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff7f7f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> key blue:0 #7f7fff:2 white:4 #ff7f7f:6 #fff6c0:8 showTool true
> color sample #33.1 map #34 palette
> 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ffad7f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> color sample #33.1 map #34 palette
> 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> key blue:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> color sample #33.1 map #34 palette
> 0,#fff6c0:2,#ff967f:4,#ffffff:6,#7f7fff:8,#0000ff outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> color sample #33.1 map #34 palette
> 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> key blue:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> color sample #33.1 map #34 palette
> 0,#00a7ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> key #00a7ff:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> color sample #33.1 map #34 palette
> 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.269, maximum 35.43
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow2.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J288_map_locres.mrc"
Opened cryosparc_P4_J288_map_locres.mrc as #36, grid size 320,320,320, pixel
0.831, shown at level 8.93, step 2, values float32
> hide #35 models
> show #35 models
> hide #!36 models
> hide #!33 models
> show #!33 models
> rename #36 cryosparc_P4_J288_map_locres_forJ285
> hide #!33 models
> show #!32 models
> hide #35 models
> show #!36 models
> select add #36
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.54984,-0.77769,0.30476,129.28,-0.81459,-0.57994,-0.010221,331.17,0.18469,-0.24264,-0.95237,263.23
> ui mousemode right "translate selected models"
> view matrix models
> #36,0.54984,-0.77769,0.30476,119.97,-0.81459,-0.57994,-0.010221,318.58,0.18469,-0.24264,-0.95237,280.96
> volume #36 level 6.234
> select subtract #36
Nothing selected
> ui tool show "Surface Color"
> color sample #32.1 map #36 palette
> 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> hide #!36 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!32 models
> show #!32 models
> hide #!33 models
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> show #!36 models
> hide #!36 models
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 white:
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8
Fetching compressed palette custom from
https://www.colourlovers.com/api/palettes?keywords=custom&format=json&numResults=100
Could not find palette custom at COLOURlovers.com using keyword search
> color sample #32.1 map #36 palette
> 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> hide #!32 models
> show #35 models
> show #!32 models
> select add #35
1 model selected
> view matrix models #35,1,0,0,-1.208,0,1,0,-1.3654,0,0,1,1.1486
> select subtract #35
Nothing selected
> select add #35
1 model selected
> select subtract #35
Nothing selected
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> ui mousemode right "color key"
> select add #35
1 model selected
> show #35
> view W35
Expected an objects specifier or a view name or a keyword
> view #35
No displayed objects specified.
> close #35
> key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true
> ui mousemode right "color key"
> hide #!32 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> volume #33 level 0.06991
> hide #!33 models
> show #!32 models
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow2.cxs"
> color sample #32.1 map #36 palette
> 0,#00a7ff:2,#99bfe5:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> key #00a7ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true
> ui mousemode right "color key"
> color sample #32.1 map #36 palette
> 0,#00a7ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#d2a5ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> key #d2a5ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true
> view #35
No objects specified.
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> key #e7c4ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow2.cxs"
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#99bfe5:4,#5da0ff:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#e0bfe8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#e0dee8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#e0dee8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#6676ed:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#6676ed:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#99bfe5:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#99bfe5:4,#6676ed:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#99bfe5:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#799bea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#5756ea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#e7c4ff:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#ffdedd:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#ffc9a3:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> color sample #32.1 map #36 palette
> 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.33, maximum 41.38
> key #ffb17f:0 #527dea:2 #99bfe5:4 #fff6c0:6 #f4fff3:8 showTool true
> ui mousemode right "color key"
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260502_SA-F_B1_workflow3.cxs"
> hide #!32 models
> show #!33 models
> hide #!33 models
> show #!32 models
> hide #!32 models
> show #!33 models
> hide #!33 models
> show #!32 models
> volume #34 step 1
> volume #36 step 1
> show #!36 models
> volume flip #36
Opened cryosparc_P4_J288_map_locres_forJ285 z flip as #38, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> hide #37 models
> ui mousemode right "rotate selected models"
> hide #!32 models
> show #!32 models
> hide #!38 models
> show #!38 models
> select add #38
2 models selected
> view matrix models
> #38,-0.22965,0.94651,-0.22667,61.099,-0.95753,-0.26145,-0.12161,309.34,-0.17437,0.18912,0.96635,13.289
> view matrix models
> #38,-0.47581,-0.84028,-0.25987,345.82,0.86453,-0.50117,0.037622,69.811,-0.16185,-0.20677,0.96491,66.334
> view matrix models
> #38,-0.72836,0.6263,-0.27792,180.88,-0.55109,-0.77649,-0.30556,349.01,-0.40718,-0.069403,0.91071,88.496
> view matrix models
> #38,-0.422,0.88275,-0.20657,93.707,-0.7937,-0.46985,-0.38638,351.04,-0.43814,0.0009021,0.89891,84.657
> fitmap #38 inMap #32
Fit map cryosparc_P4_J288_map_locres_forJ285 z flip in map
CS_P4_J285_sharp_flip.mrc using 1112104 points
correlation = 0.2781, correlation about mean = -0.02765, overlap = 7.665e+04
steps = 172, shift = 16.7, angle = 11.9 degrees
Position of cryosparc_P4_J288_map_locres_forJ285 z flip (#38) relative to
CS_P4_J285_sharp_flip.mrc (#32) coordinates:
Matrix rotation and translation
-0.15731459 0.96448973 -0.21215945 50.76791567
-0.83839054 -0.24396591 -0.48742375 323.17714111
-0.52187488 0.10119361 0.84699849 86.68679965
Axis 0.30630695 0.16117090 -0.93818974
Axis point 169.99659509 146.99779714 0.00000000
Rotation angle (degrees) 106.08964492
Shift along axis -13.69134858
> ui mousemode right "translate selected models"
> view matrix models
> #38,-0.29391,0.88572,-0.35933,106.9,-0.78003,-0.43953,-0.4454,363.34,-0.55243,0.14938,0.82006,93.87
> ui mousemode right "rotate selected models"
> volume #38 level 4.082
> view matrix models
> #38,-0.44764,0.81063,-0.37749,140.89,-0.70715,-0.57929,-0.40543,367.19,-0.54732,0.085454,0.83255,100.3
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models
> #38,-0.44764,0.81063,-0.37749,135.23,-0.70715,-0.57929,-0.40543,367.93,-0.54732,0.085454,0.83255,97.332
> view matrix models
> #38,-0.44764,0.81063,-0.37749,134.86,-0.70715,-0.57929,-0.40543,366.07,-0.54732,0.085454,0.83255,96.949
> select subtract #38
Nothing selected
> hide #!38 models
> color sample #32.1 map #38 palette
> 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.286, maximum 42.51
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/CS_P4_J282_sharp_flip.mrc"
Opened CS_P4_J282_sharp_flip.mrc as #39, grid size 320,320,320, pixel 0.831,
shown at level 0.0392, step 2, values float32
> hide #!32 models
> close #39
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #35, grid size
320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J287_map_locres.mrc"
Opened cryosparc_P4_J287_map_locres_forJ282 as #39, grid size 320,320,320,
pixel 0.831, shown at level 9.77, step 2, values float32
> volume #39 level 4.139
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J287_map_locres.mrc"
Opened cryosparc_P4_J287_map_locres_forJ282 as #40, grid size 320,320,320,
pixel 0.831, shown at level 9.77, step 2, values float32
> close #40
> color sample #35.1 map #39 palette
> 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.417, maximum 39.82
> hide #!39 models
> volume #35 step 1
> volume #35 level 0.06749
> color sample #35.1 map #39 palette
> 0,#ffb17f:1,#527dea:2,#99bfe5:3,#fff6c0:4,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 3.044, mean 3.567, maximum 40.68
> color sample #35.1 map #39 palette
> 0,#ffb17f:2,#527dea:3,#99bfe5:4,#fff6c0:5,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 3.044, mean 3.567, maximum 40.68
> color sample #35.1 map #39 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 3.044, mean 3.567, maximum 40.68
> close #32
> close #33
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow.cxs"
> close #39
> close #38
> close #36
> close #35
> show #!34 models
> hide #!34 models
> close #34
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size
320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size
320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J287_map_locres.mrc"
Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel
0.831, shown at level 9.77, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J288_map_locres.mrc"
Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel
0.831, shown at level 8.93, step 2, values float32
> rename #37 Color key id #36
Expected a keyword
> rename #37 Color_key id #36
Cannot change id of 2D overlay models (Color_key #37)
> hide #!33 models
> hide #!35 models
> volume #34 level 6.298
> volume #34 level 3.171
> volume #34 level 3.779
> hide #!34 models
> ui tool show "Surface Color"
No surface chosen for coloring
> show #!34 models
> hide #!34 models
> color sample #32.1 map #34 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.417, maximum 39.82
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
Could not find palette custom at COLOURlovers.com using keyword search
> show #37 models
> key pos 0.558738,0.385722 size 0.0255738,0.0868715
> key pos 0.723062,0.0751149
> key pos 0.862303,0.0795068
> key pos 0.846838,0.0779833
> select add #37
1 model selected
> key pos 0.819995,0.0796645
> key pos 0.812107,0.0767711
> key pos 0.825223,0.13099
> select subtract #37
Nothing selected
> undo
[Repeated 3 time(s)]
> color sample #32.1 map #34 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.417, maximum 39.82
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> show #37 models
> select add #37
1 model selected
> view matrix models
> #37,0.70959,0.62592,0.32358,0.61324,-0.29635,0.68175,-0.66888,-0.0021786,-0.63926,0.37874,0.66925,0.69431
> close #37
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> hide #!32 models
> show #!32 models
> volume #32 level 0.04587
> volume #32 level 0.04884
> key pos 0.437353,0.539212 size 0.000454748,0.0481037
> hide #36 models
> show #36 models
> close #36
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
[Repeated 1 time(s)]
> ui mousemode right "color key"
> ui mousemode right translate
> ui mousemode middle 'color key'
> key border false
> key border true
> key borderWidth 1.0
> key borderWidth 0.0
> key borderWidth 1.0
> key colorTreatment distinct
> key colorTreatment blended
> ui mousemode middle translate
> ui mousemode middle "color key"
> key borderColor #bfbfbf
> key borderColor default
> key borderColor #bfbfbf
> key borderColor #030303
> key borderColor #020202
> key borderColor #010202
> key borderColor black
> key labelColor #bfbfbf
> key labelColor default
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key fontSize 21
> key fontSize 22
> key fontSize 23
> key fontSize 24
> key bold true
> key italic true
> key italic false
> key numericLabelSpacing equal
> key numericLabelSpacing proportional
> key labelSide left/top
> key labelSide right/bottom
> key justification left
> key labelSide right/bottom
> key justification decimal
> key justification right
> key justification left
> key labelOffset 1.0
> key labelOffset 2.0
> key labelOffset 3.0
> key labelOffset 4.0
> key labelOffset 5.0
> key labelOffset 4.0
> key labelOffset 3.0
> key labelOffset 2.0
> key ticks true
> key ticks false
> key size 0.26000,0.05000
> key size 0.27000,0.05000
> key size 0.26000,0.05000
> key size 0.25000,0.05000
> key size 0.24000,0.05000
> key size 0.23000,0.05000
> key size 0.22000,0.05000
> key size 0.22000,0.04000
> key size 0.21000,0.04000
> key size 0.20000,0.04000
> key size 0.19000,0.04000
> key bold false
> key borderWidth 2.0
> key border false
> key border true
> key size 0.18000,0.04000
> key size 0.17000,0.04000
> key size 0.17000,0.03000
> key size 0.17000,0.02000
> key size 0.16000,0.02000
> key size 0.15000,0.02000
> key size 0.14000,0.02000
> key size 0.15000,0.02000
> key size 0.14000,0.02000
> key size 0.14000,0.01000
> key size 0.14000,0.02000
> key size 0.14000,0.01000
> key size 0.14000,0.02000
> key size 0.14000,0.03000
> key size 0.14000,0.04000
> key size 0.14000,0.03000
> key bold true
> save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true
> hide #!32 models
> show #!33 models
> show #!35 models
> volume #33 level 0.0299
> undo
> show #!35 models
> volume #35 level 3.774
> hide #!35 models
> color sample #33.1 map #35 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.383, maximum 41.2
> volume #33 level 0.03991
> volume #33 level 0.049
> volume #33 level 0.06811
> volume #33 level 0.05628
> volume #33 level 0.05719
> ui mousemode right translate
[Repeated 1 time(s)]
> select add #37
1 model selected
> ui mousemode right translate
> select subtract #37
Nothing selected
> view #33
> volume #33 level 0.05264
> volume #33 level 0.05082
> save CS_P4_J285_NU_sharp.png supersample 3 transparentBackground true
> save CS_P4_J285_locres_sharp.png supersample 3 transparentBackground true
> hide #!33 models
> show #!32 models
> volume #32 level 0.05478
> save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow1.cxs"
> show #!33 models
> hide #!33 models
> volume flip #32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #38, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> color sample #38.1 map #34 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.643, maximum 46.37
> select add #38
2 models selected
> select subtract #38
Nothing selected
> show #!34 models
> hide #!34 models
> show #!32 models
> select add #38
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #38,0.96218,0.27239,0.0026401,-33.277,0.27218,-0.96095,-0.049909,243.62,-0.011058,0.04874,-0.99875,256.5
> fitmap #38 inMap #32
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points
correlation = 0.3998, correlation about mean = 0.04433, overlap = 423.6
steps = 132, shift = 4.37, angle = 6.4 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative
to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates:
Matrix rotation and translation
0.98647244 0.16384860 0.00507628 -21.42824077
0.16385811 -0.98468453 -0.05955579 259.77996198
-0.00475960 0.05958193 -0.99821207 257.16545694
Axis 0.99660933 0.08227896 0.00007951
Axis point 0.00000000 126.91521003 132.48208787
Rotation angle (degrees) 176.57330142
Shift along axis 0.03928788
> select subtract #38
Nothing selected
> select add #38
2 models selected
> view matrix models
> #38,-0.55814,-0.81354,-0.1632,351.46,-0.79796,0.58019,-0.16319,187.27,0.22745,0.039147,-0.973,224.57
> ui mousemode right "translate selected models"
> view matrix models
> #38,-0.55814,-0.81354,-0.1632,337.55,-0.79796,0.58019,-0.16319,184.57,0.22745,0.039147,-0.973,224.6
> fitmap #38 inMap #32
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points
correlation = 0.4208, correlation about mean = 0.04628, overlap = 461.9
steps = 76, shift = 2.33, angle = 4.27 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative
to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates:
Matrix rotation and translation
-0.49732082 -0.85447621 -0.15014131 334.86076124
-0.83743504 0.51801846 -0.17423960 201.03033487
0.22665956 0.03908062 -0.97318968 225.34606158
Axis 0.49228130 -0.86954734 0.03932608
Axis point 210.12674218 0.00000000 138.36301119
Rotation angle (degrees) 167.48677512
Shift along axis -1.09772430
> select subtract #38
Nothing selected
> select add #38
2 models selected
> view matrix models
> #38,-0.49732,-0.85448,-0.15014,335.05,-0.83744,0.51802,-0.17424,201.05,0.22666,0.039081,-0.97319,225.03
> ui mousemode right "rotate selected models"
> view matrix models
> #38,-0.016367,0.99633,0.084023,-21.562,0.99914,0.013095,0.039355,-10.502,0.03811,0.084595,-0.99569,247.71
> ui mousemode right "translate selected models"
> view matrix models
> #38,-0.016367,0.99633,0.084023,-11.414,0.99914,0.013095,0.039355,-8.4507,0.03811,0.084595,-0.99569,248.91
> fitmap #38 inMap #32
Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map
cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points
correlation = 0.4638, correlation about mean = 0.04825, overlap = 549.2
steps = 212, shift = 3.48, angle = 14 degrees
Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative
to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates:
Matrix rotation and translation
-0.11733678 0.98529275 -0.12421864 36.78201449
0.98526620 0.13117004 0.10974943 -32.51895072
0.12442908 -0.10951079 -0.98616672 260.89985464
Axis -0.66139292 -0.75003960 -0.00008010
Axis point 18.21387939 0.00000000 132.49954907
Rotation angle (degrees) 170.45882216
Shift along axis 0.04223943
> select subtract #38
Nothing selected
> hide #!32 models
> color sample #38.1 map #34 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 3.043, mean 3.992, maximum 41.6
> show #!34 models
> volume flip #34
Opened cryosparc_P4_J287_map_locres.mrc z flip as #39, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> select add #39
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #39,0.92903,0.36038,-0.083822,-29.473,0.36808,-0.92323,0.1103,201.34,-0.037639,-0.13332,-0.99036,275.09
> show #!34 models
> fitmap #39 imapt #34
Expected a keyword
> fitmap #39 inMap #34
Fit map cryosparc_P4_J287_map_locres.mrc z flip in map
cryosparc_P4_J287_map_locres.mrc using 2056381 points
correlation = 0.8371, correlation about mean = 0.04941, overlap = 1.057e+08
steps = 612, shift = 15.2, angle = 38.8 degrees
Position of cryosparc_P4_J287_map_locres.mrc z flip (#39) relative to
cryosparc_P4_J287_map_locres.mrc (#34) coordinates:
Matrix rotation and translation
0.49975558 0.86379414 -0.06406286 -38.69544656
0.86380943 -0.49157793 0.11038297 66.86486459
0.06385627 -0.11050260 -0.99182234 270.06743869
Axis -0.86536171 -0.50114779 0.00005993
Axis point 0.00000000 54.63554700 132.55703766
Rotation angle (degrees) 172.66756182
Shift along axis -0.00743630
> select subtract #39
Nothing selected
> hide #!39 models
> show #!39 models
> select add #39
2 models selected
> hide #37 models
> hide #!38 models
> view matrix models
> #39,0.37237,-0.92808,0.0029165,218.26,-0.92659,-0.37195,-0.055474,318.12,0.052569,0.017955,-0.99846,254.69
> ui mousemode right "translate selected models"
> view matrix models
> #39,0.37237,-0.92808,0.0029165,208.8,-0.92659,-0.37195,-0.055474,313.9,0.052569,0.017955,-0.99846,255.36
> ui mousemode right "rotate selected models"
> view matrix models
> #39,0.66947,-0.74091,0.05349,135.56,-0.73453,-0.67101,-0.10103,334.54,0.11074,0.028346,-0.99344,245.27
> ui mousemode right "translate selected models"
> view matrix models
> #39,0.66947,-0.74091,0.05349,211.58,-0.73453,-0.67101,-0.10103,368.3,0.11074,0.028346,-0.99344,245.76
> view matrix models
> #39,0.66947,-0.74091,0.05349,241.5,-0.73453,-0.67101,-0.10103,381.69,0.11074,0.028346,-0.99344,243.08
> view matrix models
> #39,0.66947,-0.74091,0.05349,287.43,-0.73453,-0.67101,-0.10103,402.31,0.11074,0.028346,-0.99344,237.25
> ui mousemode right "rotate selected models"
> view matrix models
> #39,-0.41494,0.89077,-0.18535,241.42,0.8738,0.44692,0.19168,-11.043,0.25358,-0.082424,-0.9638,229.13
> view matrix models
> #39,0.99948,-0.019992,0.025148,145.79,-0.021975,-0.99645,0.081215,326.06,0.023435,-0.081726,-0.99638,264.88
> ui mousemode right "translate selected models"
> view matrix models
> #39,0.99948,-0.019992,0.025148,-4.0949,-0.021975,-0.99645,0.081215,259.26,0.023435,-0.081726,-0.99638,270.42
> select subtract #39
Nothing selected
> hide #!34 models
> color sample #38.1 map #34 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 3.043, mean 3.992, maximum 41.6
> hide #!39 models
> show #!38 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #40, grid size
320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32
> hide #!38 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J287_map_locres.mrc"
Opened cryosparc_P4_J287_map_locres.mrc as #41, grid size 320,320,320, pixel
0.831, shown at level 9.77, step 2, values float32
> volume flip #40
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #42, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #41
Opened cryosparc_P4_J287_map_locres.mrc z flip as #43, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> volume #43 level 4.042
> color sample #42.1 map #43 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.484, maximum 42.57
> hide #!43 models
> hide #!42 models
> show #!38 models
> show #!39 models
> show #!40 models
> show #!41 models
> show #!42 models
> show #!43 models
> close #43
> close #38
> close #42
> close #41
> close #40
> close #39
> close #37
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> hide #36 models
> volume flip #32
Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #34
Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> volume flip #33
Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #35
Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> hide #!39 models
> hide #!40 models
> hide #!38 models
> color sample #37.1 map #38 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.731, maximum 41.43
> hide #!37 models
> show #!37 models
> hide #!37 models
> show #!39 models
> color sample #39.1 map #40 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.67, maximum 40.73
> volume #39 level 0.05082
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> show #36 models
> select add #36
1 model selected
> key pos 0.366468,0.16715
> key pos 0.360149,0.168599
> key labelColor #bfbfbf
> key labelColor default
> key labelColor #bfbfbf
> key labelColor white
> key labelColor default
> key ticks true
> key tickLength 8.0
> key tickThickness 3.0
> key tickThickness 2.0
> key tickThickness 1.0
> key tickLength 10.0
> key tickLength 8.0
> key tickThickness 2.0
> key tickThickness 1.0
> key tickThickness 0.0
> key tickThickness 1.0
> key tickThickness 2.0
> key ticks false
> key labelOffset -1.0
> key labelOffset -2.0
> key labelOffset -1.0
> key labelOffset 0.0
> key labelOffset 1.0
> key labelOffset 2.0
> key labelOffset 3.0
> key labelOffset 4.0
> view matrix models #36,1,0,0,-0.86321,0,1,0,-0.41592,0,0,1,0.9887
> select subtract #36
Nothing selected
> select add #36
1 model selected
> view matrix models #36,1,0,0,-99.598,0,1,0,-41.849,0,0,1,63.569
> view matrix models #36,1,0,0,-99.715,0,1,0,-41.895,0,0,1,63.621
> view matrix models #36,1,0,0,-102.61,0,1,0,-42.915,0,0,1,63.831
> view matrix models #36,1,0,0,-126.49,0,1,0,-56.195,0,0,1,105.79
> view matrix models #36,1,0,0,-152.42,0,1,0,-56.013,0,0,1,31.21
> view matrix models #36,1,0,0,-131.29,0,1,0,-47.985,0,0,1,24.738
> view matrix models #36,1,0,0,-121.36,0,1,0,-44.649,0,0,1,25.261
> view matrix models #36,1,0,0,-121.37,0,1,0,-44.69,0,0,1,25.567
> view matrix models #36,1,0,0,-123.18,0,1,0,-45.336,0,0,1,25.776
> close #36
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> key pos 0.377773,0.195303
> key pos 0.377554,0.185959
> key borderWidth 3.0
> key labelOffset 1.0
> key labelOffset 2.0
> key labelOffset 3.0
> key labelOffset 4.0
> key labelOffset 5.0
> key labelOffset 6.0
> key size 0.24000,0.05000
> key size 0.23000,0.05000
> key size 0.23000,0.04000
> key size 0.23000,0.03000
> key size 0.22000,0.03000
> key size 0.21000,0.03000
> key size 0.20000,0.03000
> key size 0.19000,0.03000
> key size 0.18000,0.03000
> key size 0.17000,0.03000
> key size 0.16000,0.03000
> key size 0.15000,0.03000
> key size 0.16000,0.03000
> key size 0.17000,0.03000
> key size 0.17000,0.04000
> key size 0.17000,0.05000
> key size 0.17000,0.04000
> key pos 0.36134,0.205524 size 0.0323267,0.199875
> key pos 0.375585,0.243532 size 0.000780577,0.00120384
> key pos 0.393081,0.282969 size 0,0
[Repeated 1 time(s)]
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> hide #!39 models
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> key pos 0.654167,0.35194 size 0.0389145,0.208023
> show #!39 models
> key pos 0.434243,0.168612 size 0.0379186,0.161115
> hide #41 models
> ui mousemode right "translate selected models"
> ui mousemode right translate
[Repeated 1 time(s)]
> select add #41
1 model selected
> select subtract #41
Nothing selected
> show #41 models
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right select
> select clear
> ui mousemode right rotate
> ui mousemode right translate
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
[Repeated 1 time(s)]
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right select
> select clear
> select add #41
1 model selected
> select clear
Drag select of 39 cryosparc_P4_J285_006_volume_map_sharp.mrc z flip
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> select clear
Drag select of 39 cryosparc_P4_J285_006_volume_map_sharp.mrc z flip
> ui mousemode right translate
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> select subtract #41
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right rotate
> ui mousemode right translate
> hide #!39 models
> show #!39 models
> ui mousemode right select
> select #39
2 models selected
> ui mousemode right rotate
> ui mousemode right translate
> select subtract #39
Nothing selected
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> hide #!39 models
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode left "color key"
> ui mousemode left rotate
> ui mousemode right 'color key'
> key pos 0.683937,0.290603 size 0.0366198,0.178803
> show #!39 models
> key pos 0.885363,0.663755 size 0.0185522,0.00687018
> ui mousemode right translate
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> key pos 0.768821,0.24433 size 0.0347996,0.266198
> key labelOffset 7.0
> key labelOffset 8.0
> key labelOffset 9.0
> hide #!39 models
> show #!37 models
> volume #37 level 0.06504
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow2.cxs"
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> key fontSize 25
> key fontSize 26
> key fontSize 27
> key fontSize 28
> key fontSize 29
> key fontSize 30
> key fontSize 31
> key fontSize 32
> key fontSize 33
> key fontSize 34
> key fontSize 35
> save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true
> hide #!37 models
> show #!39 models
> volume #39 level 0.06897
> volume #39 level 0.06638
> save CS_P4_J285_locres_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow2.cxs"
> hide #!39 models
> hide #41 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/CS_P4_J282_sharp_flip.mrc"
Opened CS_P4_J282_sharp_flip.mrc as #42, grid size 320,320,320, pixel 0.831,
shown at level 0.0392, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe University/19. Model Building/2. AcrF
> Project/2. Bound-form/SA-F_B1/Model/aligned_model_for_J282.pdb"
Chain information for aligned_model_for_J282.pdb #43
---
Chain | Description
A B C | No description available
> hide #!42 models
> select #43/BC
Nothing selected
> select #43/B, C
15672 atoms, 15966 bonds, 2068 residues, 1 model selected
> delete sel
> show #!42 models
> volume zone #42 nearAtoms #43/A
> color #43 #FFF6C0
> volume zone #42 nearAtoms #43/A distance 5
Expected a keyword
> color zone #42 near #43/A distance 5
> color zone #42 near #43/A distance 5 tran 50
Expected a keyword
> color zone #42 near #43/A distance 5 tran 50
Expected a keyword
> color #43 #FFF6C0
> color zone #42 near #43/A distance 5
> color #43 #FFF6C0 transparency 50
> color zone #42 near #43/A distance 5
> graphics silhouettes false
> lighting full
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> graphics silhouettes false
> color #42 #99bfe580 models
> hide #43 models
> transparency #42 50
> lighting soft
> volume #42 level 0.0232
> lighting soft
> close #42
> close #43
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_02_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #36, grid size
128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J242_class_01_00122_volume_sharp.mrc"
Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size
128,128,128, pixel 2.08, shown at level 0.178, step 1, values float32
> close #36
> show #!9 models
> select add #42
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #42,0.026241,-0.92593,0.37678,198.52,-0.063177,0.37462,0.92502,-34.721,-0.99766,-0.048078,-0.048667,279.22
> ui mousemode right "translate selected models"
> view matrix models
> #42,0.026241,-0.92593,0.37678,198.7,-0.063177,0.37462,0.92502,-33.267,-0.99766,-0.048078,-0.048667,263
> fitmap #42 inMap #9
Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20960 points
correlation = 1, correlation about mean = 1, overlap = 1571
steps = 128, shift = 5.08, angle = 27.9 degrees
Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#42) relative
to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.99999999 -0.00010909 0.00000609 0.02020954
0.00010909 0.99999995 0.00031305 -0.06272325
-0.00000612 -0.00031305 0.99999995 0.03217050
Axis -0.94414385 0.01842055 0.32901836
Axis point 0.00000000 112.87704178 199.81299213
Rotation angle (degrees) 0.01899762
Shift along axis -0.00965143
> select subtract #42
Nothing selected
> select add #42
2 models selected
> fitmap #42 inMap #9
Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map
cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20960 points
correlation = 1, correlation about mean = 1, overlap = 1571
steps = 40, shift = 0.00318, angle = 0.00769 degrees
Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#42) relative
to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.99999999 -0.00011772 0.00012933 0.00283694
0.00011769 0.99999996 0.00026066 -0.05912201
-0.00012937 -0.00026064 0.99999996 0.04294746
Axis -0.83040251 0.41209275 0.37498166
Axis point 0.00000000 180.01203882 210.06369623
Rotation angle (degrees) 0.01798432
Shift along axis -0.01061505
> select subtract #42
Nothing selected
> hide #!9 models
> volume #42 level 0.2579
> color #42 #ffffb2ff models
> color #42 #ffffb280 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/CS_P4_J282_sharp_flip.mrc"
Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831,
shown at level 0.0392, step 2, values float32
> volume #42 level 0.1954
> select add #42
2 models selected
> view matrix models
> #42,0.15189,-0.98482,-0.084022,248.42,-0.056394,-0.093504,0.99402,24.018,-0.98679,-0.14625,-0.069741,273.86
> volume #42 level 0.2537
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_03_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32
> close #43
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J169_class_02_00182_volume_sharp.mrc"
Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size
128,128,128, pixel 2.08, shown at level 0.216, step 1, values float32
> select add #43
4 models selected
> view matrix models
> #42,0.15189,-0.98482,-0.084022,246.73,-0.056394,-0.093504,0.99402,-45.124,-0.98679,-0.14625,-0.069741,235.92,#43,1,0,0,-1.6882,0,1,0,-69.141,0,0,1,-37.947
> view matrix models
> #42,0.15189,-0.98482,-0.084022,237,-0.056394,-0.093504,0.99402,126.12,-0.98679,-0.14625,-0.069741,312.08,#43,1,0,0,-11.419,0,1,0,102.11,0,0,1,38.221
> select subtract #42
2 models selected
> view matrix models #43,1,0,0,-10.922,0,1,0,105.75,0,0,1,25.23
> ui mousemode right "rotate selected models"
> view matrix models
> #43,0.053361,-0.96815,-0.24461,270.41,-0.10024,-0.24891,0.96332,141.36,-0.99353,-0.026885,-0.11033,315.47
> ui mousemode right "translate selected models"
> view matrix models
> #43,0.053361,-0.96815,-0.24461,276.43,-0.10024,-0.24891,0.96332,50.344,-0.99353,-0.026885,-0.11033,257.37
> ui mousemode right "rotate selected models"
> view matrix models
> #43,0.25016,-0.91768,-0.30868,252.37,-0.0074281,-0.32063,0.94718,48.872,-0.96818,-0.23465,-0.087026,276.42
> ui mousemode right "translate selected models"
> view matrix models
> #43,0.25016,-0.91768,-0.30868,252.17,-0.0074281,-0.32063,0.94718,49.119,-0.96818,-0.23465,-0.087026,280.28
> view matrix models
> #43,0.25016,-0.91768,-0.30868,245.18,-0.0074281,-0.32063,0.94718,41.479,-0.96818,-0.23465,-0.087026,278.46
> view matrix models
> #43,0.25016,-0.91768,-0.30868,244.24,-0.0074281,-0.32063,0.94718,46.881,-0.96818,-0.23465,-0.087026,278.05
> select add #42
4 models selected
> select subtract #43
2 models selected
> view matrix models
> #42,0.15189,-0.98482,-0.084022,248.26,-0.056394,-0.093504,0.99402,10.768,-0.98679,-0.14625,-0.069741,272.27
> select subtract #42
Nothing selected
> color #36 #99BFE5
> hide #!42 models
> select add #43
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #43,0.073784,-0.55439,0.82898,66.918,0.0052521,0.83145,0.55558,-43.45,-0.99726,-0.036639,0.064259,236.72
> ui mousemode right "translate selected models"
> view matrix models
> #43,0.073784,-0.55439,0.82898,82.905,0.0052521,0.83145,0.55558,-39.115,-0.99726,-0.036639,0.064259,236.78
> select subtract #43
Nothing selected
> volume #36 level 0.0602
> select add #43
2 models selected
> view matrix models
> #43,0.073784,-0.55439,0.82898,84.941,0.0052521,0.83145,0.55558,-38.546,-0.99726,-0.036639,0.064259,236.53
> view matrix models
> #43,0.073784,-0.55439,0.82898,84.833,0.0052521,0.83145,0.55558,-38.074,-0.99726,-0.036639,0.064259,236.34
> volume #43 level 0.1902
> color #43 #b2b2ff80 models
> volume #43 level 0.2283
> select add #40
4 models selected
> select subtract #40
2 models selected
> select subtract #43
Nothing selected
> color #43 #ffffb280 models
> color #43 #b2b2ff80 models
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow3.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_cryosparc_P4_J243_003_volume_map_35_TMD_regions_resampled.mrc"
Opened
cryosparc_P4_cryosparc_P4_J243_003_volume_map_35_TMD_regions_resampled.mrc as
#44, grid size 80,80,80, pixel 3.32, shown at level 0.324, step 1, values
float32
> close #44
> save CS_P4_J282_show_mask_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260503_SA-F_B1_workflow4.cxs"
——— End of log from Sun May 3 17:29:06 2026 ———
> view name session-start
opened ChimeraX session
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J295_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J295_006_volume_map_sharp.mrc as #44, grid size
320,320,320, pixel 0.831, shown at level 0.0361, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J296_map_locres.mrc"
Opened cryosparc_P4_J296_map_locres.mrc as #45, grid size 320,320,320, pixel
0.831, shown at level 8.66, step 2, values float32
> hide #!43 models
> hide #!36 models
> hide #!45 models
> show #!45 models
> hide #!45 models
> volume flip #44
Opened cryosparc_P4_J295_006_volume_map_sharp.mrc z flip as #46, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #45
Opened cryosparc_P4_J296_map_locres.mrc z flip as #47, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> close #45
> close #44
> rename #46 CS_P4_J295_sharp_flip id #44
> save CS_P4_J295_sharp_flip.mrc #44
> rename #47 CS_P4_J296_locres_flip id #45
> save CS_P4_J296_locres_flip.mrc #45
> ui tool show "Surface Color"
> hide #!45 models
> color sample #44.1 map #45 palette #ffb17f:#527dea:#99bfe5:#fff6c0:#f4fff3
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.132, maximum 48.35
> show #41 models
> volume #44 level 0.0515
> color sample #44.1 map #45 palette
> 1,#ffb17f:2,#527dea:3,#99bfe5:4,#fff6c0:5,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#ffb17f:3,#527dea:4,#ffb17f:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#527dea:3,#99bfe5:4,#ffb17f:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> key #527dea:2 #99bfe5:3 #ffb17f:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#527dea outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> key #f4fff3:2 #fff6c0:3 #ffb17f:4 #99bfe5:5 #527dea:6 showTool true
> ui mousemode right "color key"
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#527dd6 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#46a2de outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#4d8fde outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#94aec1 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#a78bc1 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#c1a77f outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#89b3c1 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> color sample #44.1 map #45 palette
> 2,#ffb17f:3,#2c98ee:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> color sample #44.1 map #45 palette
> 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 3.583, maximum 39.22
> save CS_P4_J295_locres_sharp.png supersample 3 transparentBackground true
Cell requested for row 0 is out of bounds for table with 6 rows! Resizing
table model.
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260505_SA-F_B1_workflow.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J300_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J300_005_volume_map_sharp.mrc as #46, grid size
320,320,320, pixel 0.831, shown at level 0.0375, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J301_map_locres.mrc"
Opened cryosparc_P4_J301_map_locres.mrc as #47, grid size 320,320,320, pixel
0.831, shown at level 9.68, step 2, values float32
> hide #!44 models
> hide #!47 models
> volume flip #46
Opened cryosparc_P4_J300_005_volume_map_sharp.mrc z flip as #48, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #47
Opened cryosparc_P4_J301_map_locres.mrc z flip as #49, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> close #46
> close #47
> rename #48 CS_P4_J300_sharp_flip id #46
> rename #49 CS_P4_J301_locres_flip id #47
> save CS_P4_J301_locres_flip.mrc #47
> save CS_P4_J300_sharp_flip.mrc #46
> color sample #46.1 map #47 palette
> 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.498, maximum 44.88
> hide #!47 models
> volume #46 level 0.03399
> volume #46 level 0.06962
> volume #46 level 0.05919
> save CS_P4_J300_locres_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260505_SA-F_B1_workflow.cxs"
——— End of log from Tue May 5 09:31:57 2026 ———
> view name session-start
opened ChimeraX session
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J302_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J302_002_volume_map_sharp.mrc as #48, grid size 80,80,80,
pixel 3.32, shown at level 0.658, step 1, values float32
> select add #48
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #48,0.064602,0.97911,0.19278,-26.266,0.98732,-0.034646,-0.1549,22.036,-0.14498,0.20034,-0.96894,229.94
> volume flip #48
Opened cryosparc_P4_J302_002_volume_map_sharp.mrc z flip as #49, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #48
> rename #49 rename
> rename #49 CS_P4_J302_sharp_flip id #48
> save CS_P4_J302_sharp_flip.mrc #48
> select add #48
2 models selected
> view matrix models
> #48,-0.56486,-0.82475,0.026783,324.58,0.77395,-0.54076,-0.32951,143.72,0.28625,-0.1654,0.94377,-52.222
> hide #41 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!45 models
> hide #!45 models
> show #!43 models
> hide #!43 models
> show #!39 models
> ui mousemode right "translate selected models"
> view matrix models
> #48,-0.56486,-0.82475,0.026783,319.51,0.77395,-0.54076,-0.32951,139.04,0.28625,-0.1654,0.94377,-3.8614
> view matrix models
> #48,-0.56486,-0.82475,0.026783,321.32,0.77395,-0.54076,-0.32951,140.03,0.28625,-0.1654,0.94377,-10.821
> fitmap $48 inmap #39
Missing or invalid "atomsOrMap" argument: invalid objects specifier
> fitmap #48 inMap #39
Fit map CS_P4_J302_sharp_flip.mrc in map
cryosparc_P4_J285_006_volume_map_sharp.mrc z flip using 5112 points
correlation = 0.3608, correlation about mean = 0.02111, overlap = 103.8
steps = 76, shift = 4.71, angle = 3.71 degrees
Position of CS_P4_J302_sharp_flip.mrc (#48) relative to
cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#39) coordinates:
Matrix rotation and translation
-0.54436883 -0.83749052 0.04766738 317.13056079
0.79848148 -0.53475206 -0.27652762 129.04232256
0.25707950 -0.11247150 0.95982304 -11.58663120
Axis 0.09898047 -0.12634523 0.98703584
Axis point 124.28808276 149.04371086 0.00000000
Rotation angle (degrees) 124.03152255
Shift along axis 3.64942894
> ui mousemode right "rotate selected models"
> view matrix models
> #48,-0.38435,0.91427,-0.12797,86.018,-0.92117,-0.38898,-0.012326,307,-0.061046,0.11314,0.9917,-2.8083
> fitmap #48 inMap #39
Fit map CS_P4_J302_sharp_flip.mrc in map
cryosparc_P4_J285_006_volume_map_sharp.mrc z flip using 5112 points
correlation = 0.623, correlation about mean = 0.1973, overlap = 254
steps = 104, shift = 5.55, angle = 8.62 degrees
Position of CS_P4_J302_sharp_flip.mrc (#48) relative to
cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#39) coordinates:
Matrix rotation and translation
-0.49090927 0.85957769 -0.14189522 105.36638005
-0.85910240 -0.50468247 -0.08508012 328.20339808
-0.14474501 0.08013591 0.98621858 12.70754555
Axis 0.09568836 0.00165051 -0.99540997
Axis point 147.88121154 133.69042072 0.00000000
Rotation angle (degrees) 120.31054935
Shift along axis -2.02517664
> select subtract #48
Nothing selected
> volume #48 level 0.8066
> hide #!48 models
> show #!48 models
> hide #!39 models
> show #!40 models
> hide #!40 models
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> volume #48 level 0.6121
> show #!24 models
> hide #!24 models
> color #48 #99BFE5
> hide #!48 models
> show #!48 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J303_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J303_003_volume_map_sharp.mrc as #49, grid size 80,80,80,
pixel 3.32, shown at level 0.57, step 1, values float32
> select add #49
2 models selected
> view matrix models
> #49,0.53874,0.84077,0.053573,-61.438,0.83514,-0.54134,0.097405,87.116,0.1109,-0.0077344,-0.9938,260.56
> view matrix models
> #49,0.53215,0.84494,0.053856,-61.154,0.83957,-0.53484,0.095262,85.896,0.10929,-0.0054773,-0.99399,260.49
> view matrix models
> #49,-0.8763,-0.44891,0.17485,296.18,-0.45964,0.88777,-0.024369,82.131,-0.14428,-0.10172,-0.98429,307.41
> volume flip #49
Opened cryosparc_P4_J303_003_volume_map_sharp.mrc z flip as #50, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #49
> rename #50 CS_P4_J303_sharp_flip id #49
> save CS_P4_J303_sharp_flip.mrc #49
> select add #49
2 models selected
> view matrix models
> #49,-0.44927,0.88595,-0.11509,87.376,-0.86051,-0.46376,-0.21085,349.13,-0.24018,0.0043123,0.97072,61.749
> ui mousemode right "translate selected models"
> view matrix models
> #49,-0.44927,0.88595,-0.11509,93.572,-0.86051,-0.46376,-0.21085,352.06,-0.24018,0.0043123,0.97072,37.843
> fitmap #49 inMap 348
Invalid "inMap" argument: invalid density map specifier
> fitmap #49 inMap #48
Fit map CS_P4_J303_sharp_flip.mrc in map CS_P4_J302_sharp_flip.mrc using 5118
points
correlation = 0.8483, correlation about mean = 0.4386, overlap = 3011
steps = 68, shift = 10.7, angle = 7.19 degrees
Position of CS_P4_J303_sharp_flip.mrc (#49) relative to
CS_P4_J302_sharp_flip.mrc (#48) coordinates:
Matrix rotation and translation
0.99996126 -0.00401528 0.00783497 -1.22617333
0.00399514 0.99998870 0.00258400 -1.26181412
-0.00784526 -0.00255260 0.99996598 1.34185977
Axis -0.28004899 0.85489100 0.43673098
Axis point 178.64594040 0.00000000 162.72002408
Rotation angle (degrees) 0.52546068
Shift along axis -0.14929320
> select subtract #49
Nothing selected
> hide #!48 models
> color #49 #FCEDFF
> hide #!49 models
> show #!49 models
> volume #49 level 0.5753
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J304_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J304_002_volume_map_sharp.mrc as #50, grid size 80,80,80,
pixel 3.32, shown at level 1.66, step 1, values float32
> hide #!49 models
> select add #50
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #50,0.25626,0.96633,0.023099,-33.544,0.9662,-0.25539,-0.035012,44.222,-0.027934,0.03129,-0.99912,256.23
> volume #50 level 2.579
> select subtract #50
Nothing selected
> volume #50 level 1.975
> volume flip #50
Opened cryosparc_P4_J304_002_volume_map_sharp.mrc z flip as #51, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #50
> rename #51 CS_P4_J304_sharp_flip id #50
> save CS_P4_J304_sharp_flip.mrc #50
> select add #50
2 models selected
> show #!49 models
> view matrix models
> #50,0.25432,0.96619,0.042346,-35.759,0.96711,-0.25431,-0.0057645,40.158,0.0051995,0.042419,-0.99909,250.22
> view matrix models
> #50,-0.77557,0.61543,-0.14049,175.22,-0.61485,-0.78688,-0.052719,333.03,-0.143,0.045495,0.98868,11.993
> color #50 #FCEDFF
> select subtract #50
Nothing selected
> hide #!49 models
> hide #!50 models
> show #!50 models
> volume #50 level 1.954
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J305_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J305_003_volume_map_sharp.mrc as #51, grid size 80,80,80,
pixel 3.32, shown at level 0.569, step 1, values float32
> hide #!50 models
> select add #51
2 models selected
> view matrix models
> #51,-0.9391,-0.22026,0.26379,268.58,-0.1463,0.9508,0.27307,-8.1662,-0.31096,0.21785,-0.92512,264.01
> volume flip #51
Opened cryosparc_P4_J305_003_volume_map_sharp.mrc z flip as #52, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #51
> rename #52 CS_P4_J305_sharp_flip id #51
> save CS_P4_J305_sharp_flip.mrc #51
> color #51 #FCEDFF
> show #!50 models
> select add #51
2 models selected
> view matrix models
> #51,0.99548,-0.078687,0.053201,5.068,0.073705,0.99322,0.089881,-20.578,-0.059913,-0.085553,0.99453,15.159
> fitmap #51 inMap #50
Fit map CS_P4_J305_sharp_flip.mrc in map CS_P4_J304_sharp_flip.mrc using 5112
points
correlation = 0.7769, correlation about mean = 0.3462, overlap = 4325
steps = 92, shift = 6.39, angle = 27.1 degrees
Position of CS_P4_J305_sharp_flip.mrc (#51) relative to
CS_P4_J304_sharp_flip.mrc (#50) coordinates:
Matrix rotation and translation
-0.48191930 -0.86211205 -0.15657780 337.25915719
0.86174903 -0.49867166 0.09335524 70.84333299
-0.15856359 -0.08994107 0.98324371 36.25215794
Axis -0.10573285 0.00114549 0.99439391
Axis point 149.95468753 133.49561797 0.00000000
Rotation angle (degrees) 119.91228641
Shift along axis 0.47070508
> select subtract #51
Nothing selected
> hide #!50 models
> hide #!51 models
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J306_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J306_002_volume_map_sharp.mrc as #52, grid size 80,80,80,
pixel 3.32, shown at level 0.89, step 1, values float32
> select add #52
2 models selected
> view matrix models
> #52,0.64736,0.71151,-0.27328,-15.881,0.69766,-0.69754,-0.16345,155.65,-0.30692,-0.084848,-0.94795,287.9
> volume flip #52
Opened cryosparc_P4_J306_002_volume_map_sharp.mrc z flip as #53, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #52
> select add #53
2 models selected
> show #!51 models
> view matrix models
> #53,-0.54969,0.82414,-0.13652,114.28,-0.83504,-0.54665,0.062273,314.18,-0.023306,0.14823,0.98868,-59.023
> ui mousemode right "translate selected models"
> view matrix models
> #53,-0.54969,0.82414,-0.13652,112.71,-0.83504,-0.54665,0.062273,313.11,-0.023306,0.14823,0.98868,-22.329
> fitmap #53 inMap #51
Fit map cryosparc_P4_J306_002_volume_map_sharp.mrc z flip in map
CS_P4_J305_sharp_flip.mrc using 5118 points
correlation = 0.8696, correlation about mean = 0.2872, overlap = 4918
steps = 72, shift = 6.47, angle = 20.6 degrees
Position of cryosparc_P4_J306_002_volume_map_sharp.mrc z flip (#53) relative
to CS_P4_J305_sharp_flip.mrc (#51) coordinates:
Matrix rotation and translation
-0.48951817 0.85648171 -0.16374082 109.67271887
-0.85572951 -0.50794021 -0.09860917 331.28158536
-0.16762749 0.09184687 0.98156263 12.77250071
Axis 0.11055185 0.00225605 -0.99386780
Axis point 150.74970822 134.14339059 0.00000000
Rotation angle (degrees) 120.52723515
Shift along axis 0.17773418
> select subtract #53
Nothing selected
> hide #!51 models
> rename #53 CS_P4_J306_sharp_flip id #52
> save CS_P4_J306_sharp_flip.mrc #52
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J307_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J307_002_volume_map_sharp.mrc as #53, grid size 80,80,80,
pixel 3.32, shown at level 0.417, step 1, values float32
> hide #!52 models
> select add #53
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #53,-0.97802,-0.15767,0.13647,275.15,-0.15325,0.98728,0.042392,17.478,-0.14141,0.020547,-0.98974,260.92
> volume flip #53
Opened cryosparc_P4_J307_002_volume_map_sharp.mrc z flip as #54, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #53
> select add #54
2 models selected
> show #!51 models
> view matrix models
> #54,-0.83454,0.54308,0.09272,165.84,-0.53719,-0.83947,0.081916,314.21,0.12232,0.018554,0.99232,-51.868
> ui mousemode right "translate selected models"
> view matrix models
> #54,-0.83454,0.54308,0.09272,166.01,-0.53719,-0.83947,0.081916,312.6,0.12232,0.018554,0.99232,-21.112
> fitmap #54 inMap #51
Fit map cryosparc_P4_J307_002_volume_map_sharp.mrc z flip in map
CS_P4_J305_sharp_flip.mrc using 5118 points
correlation = 0.9157, correlation about mean = 0.3086, overlap = 1346
steps = 92, shift = 8.03, angle = 16.7 degrees
Position of cryosparc_P4_J307_002_volume_map_sharp.mrc z flip (#54) relative
to CS_P4_J305_sharp_flip.mrc (#51) coordinates:
Matrix rotation and translation
-0.49196091 0.85478647 -0.16527113 110.59805296
-0.85414546 -0.51062861 -0.09845785 330.98838770
-0.16855261 0.09272817 0.98132130 13.11747971
Axis 0.11118076 0.00190829 -0.99379837
Axis point 150.81392912 133.83273648 0.00000000
Rotation angle (degrees) 120.70607669
Shift along axis -0.10813355
> select subtract #54
Nothing selected
> rename #54 CS_P4_J307_sharp_flip id #53
> save CS_P4_J307_sharp_flip.mrc #53
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J308_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J308_003_volume_map_sharp.mrc as #54, grid size 80,80,80,
pixel 3.32, shown at level 0.487, step 1, values float32
> hide #!51 models
> hide #!53 models
> select add #54
2 models selected
> view matrix models #54,1,0,0,-2.2085,0,1,0,5.106,0,0,1,17.329
> ui mousemode right "rotate selected models"
> view matrix models
> #54,-0.97907,-0.098429,0.17813,263.99,-0.078474,0.99017,0.11581,3.2524,-0.18778,0.099408,-0.97717,270.12
> volume flip #54
Opened cryosparc_P4_J308_003_volume_map_sharp.mrc z flip as #55, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #54
> select add #55
2 models selected
> show #!53 models
> view matrix models
> #55,-0.032009,-0.99944,0.0094019,279.03,0.99475,-0.030941,0.097574,-4.0943,-0.097229,0.012476,0.99518,-8.8511
> ui mousemode right "translate selected models"
> view matrix models
> #55,-0.032009,-0.99944,0.0094019,275.5,0.99475,-0.030941,0.097574,4.3503,-0.097229,0.012476,0.99518,10.879
> fitmap #55 inMap #53
Fit map cryosparc_P4_J308_003_volume_map_sharp.mrc z flip in map
CS_P4_J307_sharp_flip.mrc using 5116 points
correlation = 0.9635, correlation about mean = 0.3444, overlap = 1309
steps = 80, shift = 11, angle = 8.02 degrees
Position of cryosparc_P4_J308_003_volume_map_sharp.mrc z flip (#55) relative
to CS_P4_J307_sharp_flip.mrc (#53) coordinates:
Matrix rotation and translation
-0.47079667 0.87008681 -0.14594324 102.09450866
-0.87101131 -0.48471046 -0.07996914 326.37268834
-0.14032031 0.08946901 0.98605553 9.07494900
Axis 0.09685875 -0.00321433 -0.99529295
Axis point 148.07793015 132.95152312 0.00000000
Rotation angle (degrees) 118.99450917
Shift along axis -0.19255539
> select subtract #55
Nothing selected
> hide #!53 models
> color #55 #fcedffff models
> rename #55 CS_P4_J308_sharp_flip id #54
> save CS_P4_J308_sharp_flip.mrc #54
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J309_002_volume_map_sharp.mrc"
Opened cryosparc_P4_J309_002_volume_map_sharp.mrc as #55, grid size 80,80,80,
pixel 3.32, shown at level 0.427, step 1, values float32
> hide #!54 models
> select add #55
2 models selected
> show #!54 models
> ui mousemode right "rotate selected models"
> view matrix models
> #55,0.72482,-0.68817,-0.032661,133.9,-0.68882,-0.72298,-0.053201,331.74,0.012998,0.061058,-0.99805,234.36
> hide #!54 models
> view matrix models
> #55,-0.98503,0.14104,0.099091,242.98,0.14443,0.98912,0.027904,-21.89,-0.094078,0.041798,-0.99469,251.29
> volume flip #55
Opened cryosparc_P4_J309_002_volume_map_sharp.mrc z flip as #56, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #55
> select add #56
2 models selected
> show #!54 models
> view matrix models
> #56,-0.63923,0.76709,0.054278,117.91,-0.76391,-0.64153,0.069883,315.42,0.088428,0.0032076,0.99608,-48.086
> ui mousemode right "translate selected models"
> view matrix models
> #56,-0.63923,0.76709,0.054278,118.17,-0.76391,-0.64153,0.069883,313.6,0.088428,0.0032076,0.99608,-18.356
> fitmap #56 inMap #54
Fit map cryosparc_P4_J309_002_volume_map_sharp.mrc z flip in map
CS_P4_J308_sharp_flip.mrc using 5111 points
correlation = 0.9585, correlation about mean = 0.3571, overlap = 1283
steps = 104, shift = 10.8, angle = 17.1 degrees
Position of cryosparc_P4_J309_002_volume_map_sharp.mrc z flip (#56) relative
to CS_P4_J308_sharp_flip.mrc (#54) coordinates:
Matrix rotation and translation
-0.48831434 -0.86312376 -0.12871093 333.56502617
0.86459679 -0.49852007 0.06285020 75.43057430
-0.11841248 -0.08059241 0.98968852 28.18171624
Axis -0.08273806 -0.00594017 0.99655362
Axis point 146.06051902 134.60897835 0.00000000
Rotation angle (degrees) 119.90563147
Shift along axis 0.03799683
> select subtract #56
Nothing selected
> hide #!54 models
> hide #!56 models
> show #!56 models
> color #56 #fcedffff models
> rename #56 CS_P4_J309_sharp_flip id #55
> save CS_P4_J309_sharp_flip.mrc #55
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J310_003_volume_map_sharp.mrc"
Opened cryosparc_P4_J310_003_volume_map_sharp.mrc as #56, grid size 80,80,80,
pixel 3.32, shown at level 0.683, step 1, values float32
> volume flip #56
Opened cryosparc_P4_J310_003_volume_map_sharp.mrc z flip as #57, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #56
> fitmap #56 inMap #52
No atoms or maps for #56
> fitmap #57 inMap #52
Fit map cryosparc_P4_J310_003_volume_map_sharp.mrc z flip in map
CS_P4_J306_sharp_flip.mrc using 5115 points
correlation = 0.769, correlation about mean = 0.3701, overlap = 4288
steps = 88, shift = 5.42, angle = 22.7 degrees
Position of cryosparc_P4_J310_003_volume_map_sharp.mrc z flip (#57) relative
to CS_P4_J306_sharp_flip.mrc (#52) coordinates:
Matrix rotation and translation
-0.48166864 -0.85899522 -0.17355843 339.66736714
0.86194402 -0.50013127 0.08319372 72.72621082
-0.15826501 -0.10952585 0.98130335 38.95738038
Axis -0.11128512 -0.00883113 0.99374928
Axis point 150.89500052 135.18260516 0.00000000
Rotation angle (degrees) 120.01642768
Shift along axis 0.27169032
> hide #!55 models
> show #!52 models
> color #57 #fcedffff models
> hide #!52 models
> save #57 CS_P4_J310_sharp_flip id #56
Cannot determine format for '#57'
> rename #57 CS_P4_J310_sharp_flip id #56
> save CS_P4_J310_sharp_flip.mrc #56
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J311_004_volume_map_sharp.mrc"
Opened cryosparc_P4_J311_004_volume_map_sharp.mrc as #57, grid size 80,80,80,
pixel 3.32, shown at level 0.525, step 1, values float32
> volume flip #57
Opened cryosparc_P4_J311_004_volume_map_sharp.mrc z flip as #58, grid size
80,80,80, pixel 3.32, shown at step 1, values float32
> close #57
> color #58 #fcedffff models
> rename #58 CS_P4_J311_sharp_flip id #57
> save CS_P4_J311_sharp_flip.mrc #57
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260506_SA-F_B1_workflow.cxs"
> view P1
> hide #!57 models
> hide #!56 models
> show #!47 models
> hide #!47 models
> show #!48 models
> save CS_P4_J302_NU_sharp.png supersample 3 transparentBackground true
> hide #!48 models
> show #!49 models
> save CS_P4_J303_NU_sharp.png supersample 3 transparentBackground true
> hide #!49 models
> show #!50 models
> save CS_P4_J304_NU_sharp.png supersample 3 transparentBackground true
> hide #!50 models
> show #!51 models
> save CS_P4_J305_NU_sharp.png supersample 3 transparentBackground true
> hide #!51 models
> show #!52 models
> volume #52 level 1.034
> save CS_P4_J306_NU_sharp.png supersample 3 transparentBackground true
> hide #!52 models
> show #!53 models
> color #53 #fcedffff models
> save CS_P4_J307_NU_sharp.png supersample 3 transparentBackground true
> hide #!53 models
> show #!54 models
> save CS_P4_J308_NU_sharp.png supersample 3 transparentBackground true
> hide #!54 models
> show #!55 models
> save CS_P4_J309_NU_sharp.png supersample 3 transparentBackground true
> hide #!55 models
> show #!56 models
> volume #56 level 0.7192
> save CS_P4_J310_NU_sharp.png supersample 3 transparentBackground true
> hide #!56 models
> show #!57 models
> save CS_P4_J311_NU_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260506_SA-F_B1_workflow.cxs"
——— End of log from Wed May 6 15:19:28 2026 ———
> view name session-start
opened ChimeraX session
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J323_006_volume_map_sharp.mrc"
Opened cryosparc_P4_J323_006_volume_map_sharp.mrc as #58, grid size
320,320,320, pixel 0.831, shown at level 0.0345, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J324_map_locres.mrc"
Opened cryosparc_P4_J324_map_locres.mrc as #59, grid size 320,320,320, pixel
0.831, shown at level 8.89, step 2, values float32
> hide #!57 models
> hide #!58 models
> show #!58 models
> hide #!59 models
> show #!59 models
> volume flip #58
Opened cryosparc_P4_J323_006_volume_map_sharp.mrc z flip as #60, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #59
Opened cryosparc_P4_J324_map_locres.mrc z flip as #61, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> close #58
> close #59
> rename #60 CS_P4_J323_sharp_flip #58
Expected a keyword
> rename #60 CS_P4_J323_sharp_flip id #58
> save CS_P4_J323_sharp_flip.mrc #58
> rename CS_P4_J324_map_locres_flip id #59
Missing or invalid "models" argument: invalid models specifier
> rename #61 CS_P4_J324_map_locres_flip id #59
> save CS_P4_J324_map_locres_flip.mrc #59
> hide #!58 models
> show #!58 models
> hide #!59 models
> volume #59 level 9.377
> hide #!59 models
> volume #58 level 0.05889
> show #!59 models
> volume #59 level 3.695
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow.cxs"
> ui tool show "Surface Color"
> hide #!58 models
> show #!58 models
> hide #!59 models
> color radial #58.1 palette #ffb17f:#4979d3:#99bfe5:#fff6c0:#f4fff3
> color sample #58.1 map #59 palette
> 166.9,#ffb17f:198,#4979d3:229.1,#99bfe5:260.3,#fff6c0:291.4,#f4fff3
> outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.552, maximum 44.59
> color sample #58.1 map #59 palette
> 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.552, maximum 44.59
> show #!59 models
> hide #!58 models
> hide #!59 models
> show #!59 models
> show #!58 models
> hide #!59 models
> show #!59 models
> hide #!59 models
> volume #58 level 0.0634
> volume #58 level 0.04264
> volume #58 level 0.07693
> volume #58 level 0.06069
> volume #58 level 0.07152
> volume #58 level 0.05889
> volume #58 level 0.05167
> volume #58 level 0.06159
> key #ffb17f:2 #4979d3:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> key pos 0.82265,0.196044 size 0.0692066,0.202924
> ui mousemode right translate
> ui mousemode right "color key"
> key pos 0.802943,0.231339 size 0.039822,0.144632
> key #ffb17f:2 #4979d3:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> key pos 0.836801,0.165731 size 0.0516869,0.238605
> show #41 models
> key pos 0.820538,0.190547 size 0.0458442,0.242723
> save CS_P4_J323_sharp_flip.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow1.cxs"
> color sample #58.1 map #59 palette
> 2,#ffb17f:3,#169bd3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> color sample #58.1 map #59 palette
> 2,#ffb17f:3,#46c7f6:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> color sample #58.1 map #59 palette
> 2,#ffb17f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> key #ffb17f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true
> ui mousemode right "color key"
> color sample #58.1 map #59 palette
> 2,#ffb17f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> key #ffb17f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true
> color sample #58.1 map #59 palette
> 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> key #13097f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true
> save CS_P4_J323_sharp_flip2.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow2.cxs"
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J329_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J329_005_volume_map_sharp.mrc as #60, grid size
320,320,320, pixel 0.831, shown at level 0.0384, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J330_map_locres.mrc"
Opened cryosparc_P4_J330_map_locres.mrc as #61, grid size 320,320,320, pixel
0.831, shown at level 9.71, step 2, values float32
> hide #!58 models
> hide #!60 models
> show #!60 models
> hide #!61 models
> volume flip #60
Opened cryosparc_P4_J329_005_volume_map_sharp.mrc z flip as #62, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #61
Opened cryosparc_P4_J330_map_locres.mrc z flip as #63, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> close #60
> close #61
> rename #62 CS_P4_J329_sharp_flip id #60
> save CS_P4_J329_sharp_flip.mrc #60
> rename #63 rename
> rename #63 CS_P4_J330_locres_flip id #61
> save CS_P4_J330_locres_flip.mrc #61
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow3.cxs"
> hide #!61 models
> color sample #58.1 map #59 palette
> 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080
Map values for surface "surface": minimum 2.944, mean 3.532, maximum 44.61
> color sample #60.1 map #61 palette
> 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.466, maximum 46.71
> volume #60 level 0.06443
> key #13097f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true
> ui mousemode right "color key"
> volume #60 level 0.05663
> save CS_P4_J329_locres_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow3.cxs"
——— End of log from Thu May 7 15:58:17 2026 ———
> view name session-start
opened ChimeraX session
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J300_005_volume_map_sharp.mrc"
Opened cryosparc_P4_J300_005_volume_map_sharp.mrc as #62, grid size
320,320,320, pixel 0.831, shown at level 0.0375, step 2, values float32
> open "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/cryosparc_P4_J301_map_locres.mrc"
Opened cryosparc_P4_J301_map_locres.mrc as #63, grid size 320,320,320, pixel
0.831, shown at level 9.68, step 2, values float32
> hide #!60 models
> hide #!63 models
> volume flip #62
Opened cryosparc_P4_J300_005_volume_map_sharp.mrc z flip as #64, grid size
320,320,320, pixel 0.831, shown at step 1, values float32
> volume flip #63
Opened cryosparc_P4_J301_map_locres.mrc z flip as #65, grid size 320,320,320,
pixel 0.831, shown at step 1, values float32
> close #62
> close #63
> rename #64 CS_P4_J300_sharp_flip id #62
> save CS_P4_J300_sharp_flip.mrc #62
> rename #65 CS_P4_J301_locres_flip id #63
> save CS_P4_J301_locres_flip.mrc #63
> show #!46 models
> show #!47 models
> hide #!47 models
> hide #!46 models
> hide #!63 models
> show #!63 models
> volume #63 level 3.952
> hide #!63 models
> volume #62 level 0.0392
> ui tool show "Surface Color"
> color sample #62.1 map #63 palette #13097f:#11b6e1:#99bfe5:#fff6c0:#ffb17f
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.383, maximum 43.37
> color sample #62.1 map #63 palette
> 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080
Map values for surface "surface": minimum 0, mean 4.383, maximum 43.37
> show #!63 models
> hide #!63 models
> hide #!62 models
> show #!62 models
> volume #62 level 0.06614
> volume #62 level 0.05745
> save CS_P4_J300_locres_sharp.png supersample 3 transparentBackground true
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow4.cxs"
> open /Users/peiyuyu/Downloads/cryosparc_P7_J110_004_volume_map_sharp.mrc
Opened cryosparc_P7_J110_004_volume_map_sharp.mrc as #64, grid size
160,160,160, pixel 1.66, shown at level 0.28, step 1, values float32
> hide #!62 models
> close #64
> save "/Users/peiyuyu/Documents/Goethe
> University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA-
> F_B1/20260507_SA-F_B1_workflow5.cxs"
——— End of log from Thu May 7 21:11:39 2026 ———
> view name session-start
opened ChimeraX session
Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable
[Repeated 1 time(s)]
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,8
Model Number: MX2F3D/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 29天16小時42分鐘
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LEN T22i-10:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 2.17.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
plotly: 6.5.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.14.0
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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