id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
20338	ChimeraX bug report submission	halle.andrews-clark@…		"{{{
The following bug report has been submitted:
Platform:        macOS-26.3-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000031bb07000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031ab04000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000319b01000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000318afe000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000317afb000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000316af8000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000315af5000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000314af2000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000313aef000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000312aec000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000311ae9000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x0000000200d29e40 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.graphics._graphics, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._webp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.segment._segment (total: 64)


{""app_name"":""ChimeraX"",""timestamp"":""2026-05-15 19:33:50.00 +0200"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 26.3 (25D125)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""BE7E9ABA-F65E-4DC9-B9E8-DAE89BB2C5D4""}
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  ""uptime"" : 650000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 502,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro17,1"",
  ""coalitionID"" : 35484,
  ""osVersion"" : {
    ""train"" : ""macOS 26.3"",
    ""build"" : ""25D125"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2026-05-15 17:00:31.6785 +0200"",
  ""codeSigningMonitor"" : 1,
  ""incident"" : ""BE7E9ABA-F65E-4DC9-B9E8-DAE89BB2C5D4"",
  ""pid"" : 38574,
  ""translated"" : true,
  ""cpuType"" : ""X86-64"",
  ""procLaunch"" : ""2026-04-22 12:20:17.0198 +0200"",
  ""procStartAbsTime"" : 6068180062453,
  ""procExitAbsTime"" : 15640806792737,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"",
  ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""},
  ""storeInfo"" : {""deviceIdentifierForVendor"":""33116714-09C9-5A00-BCA9-4034A28E2E8E"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""02E04C25-79CA-2EF6-F248-C1774882463F"",
  ""appleIntelligenceStatus"" : {""reasons"":[""siriAssetIsNotReady"",""notOptedIn"",""assetIsNotReady""],""state"":""unavailable""},
  ""developerMode"" : 1,
  ""bootProgressRegister"" : ""0x3f000000"",
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570490881,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 4294967295,
  ""codeSigningAuxiliaryInfo"" : 0,
  ""bootSessionUUID"" : ""3B7E11F8-EC7A-483F-8808-4B8A8C5E6BA1"",
  ""wakeTime"" : 17308,
  ""sleepWakeUUID"" : ""C87EB039-63F2-49BB-9AC9-842E3A0E6B26"",
  ""sip"" : ""disabled"",
  ""vmRegionInfo"" : ""0x309c000031ff is not in any region.  Bytes after previous region: 52965536707072  Bytes before following region: 52106543222273\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  "",
  ""exception"" : {""codes"":""0x0000000000000001, 0x0000309c000031ff"",""rawCodes"":[1,53446573044223],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000309c000031ff""},
  ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":38574},
  ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"",
  ""vmregioninfo"" : ""0x309c000031ff is not in any region.  Bytes after previous region: 52965536707072  Bytes before following region: 52106543222273\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  "",
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  ""faultingThread"" : 0,
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    ""uuid"" : ""3064d9b7-75d7-343e-bf98-036ded114223"",
    ""path"" : ""\/Applications\/ChimeraX-1.8.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""
  },
  {
    ""source"" : ""P"",
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    ""base"" : 6023888896,
    ""size"" : 212992,
    ""uuid"" : ""9ff84874-4ecd-3fed-ba32-23b23bfaaecc"",
    ""path"" : ""\/Applications\/ChimeraX-1.8.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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    ""base"" : 6028902400,
    ""size"" : 131072,
    ""uuid"" : ""272f9886-859c-3c84-8ea4-2bde196ca08b"",
    ""path"" : ""\/Applications\/ChimeraX-1.8.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""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 6024515584,
    ""size"" : 131072,
    ""uuid"" : ""99497e49-7155-3c86-b62e-dd8a79f1be5d"",
    ""path"" : ""\/Applications\/ChimeraX-1.8.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""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 7099645952,
    ""size"" : 4210688,
    ""uuid"" : ""08a0cdf4-85d3-328a-98ac-8a7ec48356eb"",
    ""path"" : ""\/Applications\/ChimeraX-1.8.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""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 6039584768,
    ""size"" : 147456,
    ""uuid"" : ""a66bb1e2-ecf4-3220-9c8e-a465d9305940"",
    ""path"" : ""\/Applications\/ChimeraX-1.8.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""
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    ""path"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/segment\/_segment.cpython-311-darwin.so"",
    ""name"" : ""_segment.cpython-311-darwin.so""
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    ""size"" : 0,
    ""source"" : ""A"",
    ""base"" : 0,
    ""uuid"" : ""00000000-0000-0000-0000-000000000000""
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    ""base"" : 140703409131520,
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},
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
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  }
},
  ""logWritingSignature"" : ""c999421fae40fdddce8885e3f32bdb28ada583dc"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""trmStatus"" : 1,
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""60f8ddccefea4203d95cbeef"",
      ""factorPackIds"" : [

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},
  ""reportNotes"" : [
  ""RIP register does not match crashing frame (0x0 vs 0x7FF89C982B80)""
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2c.map""

Opened S2c.map as #1, grid size 400,400,400, pixel 1.32, shown at level 0.295,
step 2, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/s2a.map""

Opened s2a.map as #2, grid size 400,400,400, pixel 1.32, shown at level 0.281,
step 2, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2b.map""

Opened S2b.map as #3, grid size 400,400,400, pixel 1.32, shown at level 0.335,
step 2, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2c.map""

Opened S2c.map as #4, grid size 400,400,400, pixel 1.32, shown at level 0.295,
step 2, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2d.map""

Opened S2d.map as #5, grid size 400,400,400, pixel 1.32, shown at level 0.306,
step 2, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2e.map""

Opened S2e.map as #6, grid size 400,400,400, pixel 1.32, shown at level 0.226,
step 2, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2f.map""

Opened S2f.map as #7, grid size 400,400,400, pixel 1.32, shown at level 0.188,
step 2, values float32  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 7 maps.  

> surface dust #1 size 13.2

> surface dust #2 size 13.2

> surface dust #3 size 13.2

> surface dust #4 size 13.2

> surface dust #5 size 13.2

> surface dust #6 size 13.2

> surface dust #7 size 13.2

> surface dust #1 size 13.2

> surface dust #2 size 13.2

> surface dust #3 size 13.2

> surface dust #4 size 13.2

> surface dust #5 size 13.2

> surface dust #6 size 13.2

> surface dust #7 size 13.2

> open ""/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39
> and exit focus mask /NU/cryosparc_P1_J49_001_volume_map.mrc""
> ""/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39 and
> exit focus mask /NU/cryosparc_P1_J49_001_volume_map_sharp.mrc""

Opened cryosparc_P1_J49_001_volume_map.mrc as #8.1, grid size 128,128,128,
pixel 3.32, shown at level 1.03, step 1, values float32  
Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #8.2, grid size
128,128,128, pixel 3.32, shown at level 1.35, step 1, values float32  

> volume #8.1 level 0.2864

> surface dust #1 size 13.2

> surface dust #2 size 13.2

> surface dust #3 size 13.2

> surface dust #4 size 13.2

> surface dust #5 size 13.2

> surface dust #6 size 13.2

> surface dust #7 size 13.2

> surface dust #8.1 size 33.2

> surface dust #8.2 size 33.2

> surface dust #1 size 13.2

> surface dust #2 size 13.2

> surface dust #3 size 13.2

> surface dust #4 size 13.2

> surface dust #5 size 13.2

> surface dust #6 size 13.2

> surface dust #7 size 13.2

> surface dust #8.1 size 33.2

> surface dust #8.2 size 33.2

> hide #!8.2 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> volume #4 level 0.08311

> volume #4 level 0.2105

> select add #8.1

2 models selected  

> ui mousemode right rotate

> ui mousemode right ""rotate selected models""

> view matrix models
> #8.1,0.0025754,0.99857,-0.053465,5.7525,0.37284,0.048651,0.92662,-58.772,0.92789,-0.02232,-0.37218,83.452

> view matrix models
> #8.1,-0.18017,0.89814,-0.40111,136.33,0.98316,0.17715,-0.044956,-21.126,0.03068,-0.40245,-0.91493,465.95

> view matrix models
> #8.1,-0.063474,0.87885,-0.47286,130.14,0.9965,0.081644,0.017976,-15.856,0.054405,-0.47007,-0.88095,468.77

> ui mousemode right translate

> ui mousemode right ""rotate selected models""

> view matrix models
> #8.1,0.022353,0.89352,-0.44847,103.8,0.99913,-0.035808,-0.021544,17.061,-0.035309,-0.4476,-0.89354,485.49

> ui mousemode right ""translate selected models""

> view matrix models
> #8.1,0.022353,0.89352,-0.44847,0.42301,0.99913,-0.035808,-0.021544,-147.26,-0.035309,-0.4476,-0.89354,355.36

> volume #4 level 0.3803

> ui mousemode right ""rotate selected models""

> view matrix models
> #8.1,0.4097,0.6881,0.59889,-247.85,0.12708,0.60706,-0.78443,51.78,-0.90332,0.39749,0.16127,144.14

> volume #8.1 level 0.6263

> view matrix models
> #8.1,0.087383,-0.74178,-0.66492,398.42,-0.34416,0.6039,-0.71893,143.23,0.93484,0.29166,-0.20252,-164.28

> view matrix models
> #8.1,0.10202,-0.8194,-0.56407,391.47,-0.26506,0.52414,-0.80933,161.91,0.95882,0.23208,-0.16372,-164.47

> view matrix models
> #8.1,0.10386,-0.83529,-0.53991,389.58,-0.24676,0.50423,-0.82756,165.99,0.9635,0.21917,-0.15375,-164.72

> view matrix models
> #8.1,-0.65595,-0.56331,0.50241,283.05,-0.70482,0.69531,-0.14061,83.732,-0.27012,-0.44634,-0.85312,398.71

> view matrix models
> #8.1,0.086651,-0.88935,0.44893,201.49,0.27163,0.45464,0.84824,-283.14,-0.95849,0.048444,0.28097,208.45

> view matrix models
> #8.1,0.052105,-0.78867,0.6126,153.26,0.36271,0.58649,0.7242,-306.73,-0.93044,0.18446,0.31662,164.98

> view matrix models
> #8.1,0.10611,-0.75183,0.65076,125.34,0.19061,0.6577,0.72876,-285.26,-0.97591,0.046711,0.2131,226.67

> ui mousemode right ""translate selected models""

> ui mousemode right ""move picked models""

> view matrix models
> #8.1,0.10611,-0.75183,0.65076,291.79,0.19061,0.6577,0.72876,-8.4476,-0.97591,0.046711,0.2131,362.25

> view matrix models
> #8.1,0.10611,-0.75183,0.65076,244.74,0.19061,0.6577,0.72876,-219.96,-0.97591,0.046711,0.2131,632.84

> view matrix models
> #8.1,0.10611,-0.75183,0.65076,246.68,0.19061,0.6577,0.72876,-224.71,-0.97591,0.046711,0.2131,636.69

> ui mousemode right ""rotate selected models""

> view matrix models
> #8.1,0.31806,-0.16268,0.93401,11.834,-0.49899,0.80895,0.31081,-19.283,-0.80613,-0.56492,0.17612,741.28

> view matrix models
> #8.1,0.53916,-0.49148,0.68393,86.78,0.023771,0.82062,0.57097,-191.12,-0.84187,-0.29159,0.45413,631.77

> view matrix models
> #8.1,-0.24334,-0.11057,-0.96362,515.65,0.69154,0.67685,-0.25229,-137.56,0.68012,-0.72777,-0.088242,502.77

> view matrix models
> #8.1,-0.70391,-0.095711,-0.70382,560.73,0.4136,0.75034,-0.51569,-37.957,0.57746,-0.65409,-0.48858,591.78

> view matrix models
> #8.1,-0.70355,-0.18675,-0.68567,576.93,0.35038,0.74827,-0.56331,-13.702,0.61826,-0.63657,-0.46101,573.21

> ui mousemode right ""move picked models""

> view matrix models
> #8.1,-0.70355,-0.18675,-0.68567,704.12,0.35038,0.74827,-0.56331,83.401,0.61826,-0.63657,-0.46101,394.56

> view matrix models
> #8.1,-0.70355,-0.18675,-0.68567,616.62,0.35038,0.74827,-0.56331,147.29,0.61826,-0.63657,-0.46101,343.58

> fitmap #8.1 inMap #4

Fit map cryosparc_P1_J49_001_volume_map.mrc in map S2c.map using 55316 points  
correlation = 0.7929, correlation about mean = 0.38, overlap = 1.865e+04  
steps = 232, shift = 38.9, angle = 13.1 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to S2c.map
(#4) coordinates:  
Matrix rotation and translation  
-0.69218461 -0.23733703 -0.68158022 617.95909860  
0.17454387 0.86129906 -0.47717750 159.04125684  
0.70029630 -0.44926057 -0.55475223 339.84370085  
Axis 0.01935687 -0.95815714 0.28558748  
Axis point 232.28797415 0.00000000 331.17813189  
Rotation angle (degrees) 133.85366479  
Shift along axis -43.36965704  
  

> select subtract #8.1

Nothing selected  

> volume #8.2 level 1.313

> hide #!8.2 models

> volume #8.1 level 0.1794

> volume #4 level 0.09372

> volume #4 level 0.2052

> show #!3 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!2 models

> color #8.1 #424242ff models

> color #8.1 #919191ff models

> color #8.1 darkgrey models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.1966

> hide #!2 models

> show #!3 models

> volume #3 level 0.1677

> volume #3 level 0.2616

> color #1 #ff40ffff models

> fitmap #8.1 inMap #4

Fit map cryosparc_P1_J49_001_volume_map.mrc in map S2c.map using 134048 points  
correlation = 0.7325, correlation about mean = 0.5665, overlap = 2.127e+04  
steps = 40, shift = 0.0275, angle = 0.00667 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to S2c.map
(#4) coordinates:  
Matrix rotation and translation  
-0.69210611 -0.23735662 -0.68165311 617.97405655  
0.17459473 0.86128797 -0.47717891 159.00866787  
0.70036120 -0.44927148 -0.55466145 339.81498218  
Axis 0.01934824 -0.95815172 0.28560623  
Axis point 232.28987029 0.00000000 331.18544036  
Rotation angle (degrees) 133.84738051  
Shift along axis -43.34444050  
  

> fitmap #8.1 inMap #4

Fit map cryosparc_P1_J49_001_volume_map.mrc in map S2c.map using 134048 points  
correlation = 0.7325, correlation about mean = 0.5665, overlap = 2.127e+04  
steps = 40, shift = 0.0126, angle = 0.00329 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to S2c.map
(#4) coordinates:  
Matrix rotation and translation  
-0.69212505 -0.23738966 -0.68162238 617.98085236  
0.17458371 0.86126341 -0.47722726 159.03653587  
0.70034524 -0.44930110 -0.55465761 339.83111420  
Axis 0.01936174 -0.95814465 0.28562903  
Axis point 232.29298165 0.00000000 331.19715854  
Rotation angle (degrees) 133.84895580  
Shift along axis -43.34918724  
  

> mmaker #8.1 to #2

No 'to' model specified  

> mmaker #8.1, #2

> matchmaker #8.1, #2

Missing or invalid ""matchAtoms"" argument: only initial part ""#8.1"" of atom
specifier valid  

> mmaker #8.1 to #2

No 'to' model specified  

> mmaker #8.1 to map #2

> matchmaker #8.1 to map #2

Invalid ""to"" argument: invalid atoms specifier  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.779, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 124, shift = 0.75, angle = 0.674 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69929659 -0.23402528 -0.67543797 617.15957487  
0.16943802 0.86369735 -0.47467636 158.91165484  
0.69446025 -0.44638444 -0.56432783 343.08985010  
Axis 0.01980732 -0.95907260 0.28246667  
Axis point 232.39979995 0.00000000 330.30493069  
Rotation angle (degrees) 134.42407860  
Shift along axis -43.27208729  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.7791, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 40, shift = 0.0204, angle = 0.00868 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69923656 -0.23393818 -0.67553029 617.14650158  
0.16948896 0.86375291 -0.47455705 158.84485588  
0.69450827 -0.44632257 -0.56431767 343.05774229  
Axis 0.01976540 -0.95908809 0.28241699  
Axis point 232.38882223 0.00000000 330.28574614  
Rotation angle (degrees) 134.41903424  
Shift along axis -43.26272695  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.7791, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 44, shift = 0.0207, angle = 0.00795 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69929203 -0.23401936 -0.67544474 617.15837896  
0.16943791 0.86370364 -0.47466496 158.90828296  
0.69446487 -0.44637536 -0.56432932 343.08718388  
Axis 0.01980556 -0.95907441 0.28246064  
Axis point 232.39903032 0.00000000 330.30326961  
Rotation angle (degrees) 134.42370272  
Shift along axis -43.27307760  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.7791, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 44, shift = 0.0254, angle = 0.00963 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69923164 -0.23392252 -0.67554080 617.14078691  
0.16948155 0.86377090 -0.47452697 158.83183567  
0.69451503 -0.44629597 -0.56433038 343.05286754  
Axis 0.01976282 -0.95909348 0.28239887  
Axis point 232.38665168 0.00000000 330.27906442  
Rotation angle (degrees) 134.41862558  
Shift along axis -43.26039591  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.7791, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 40, shift = 0.0234, angle = 0.00333 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69925824 -0.23395586 -0.67550172 617.14809957  
0.16944160 0.86376114 -0.47455900 158.87165606  
0.69449799 -0.44629738 -0.56435024 343.06665000  
Axis 0.01978502 -0.95909118 0.28240513  
Axis point 232.39247403 0.00000000 330.28714869  
Rotation angle (degrees) 134.42088043  
Shift along axis -43.27833678  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.7791, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 44, shift = 0.018, angle = 0.0027 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69926433 -0.23397681 -0.67548816 617.14637779  
0.16945124 0.86373748 -0.47459861 158.86627486  
0.69448951 -0.44633219 -0.56433315 343.06743005  
Axis 0.01978856 -0.95908408 0.28242900  
Axis point 232.39289702 0.00000000 330.28780285  
Rotation angle (degrees) 134.42138794  
Shift along axis -43.26148998  
  

> hide #!8.1 models

> hide #!8 models

> show #!7 models

> show #!6 models

> show #!5 models

> show #!4 models

> show #!2 models

> volume #!2-7 showOutlineBox true

> volume #!2-7 showOutlineBox false

> merge #2-7

Unknown command: merge #2-7  

> fitmap #3 inMap #2

Fit map S2b.map in map s2a.map using 127771 points  
correlation = 0.8481, correlation about mean = 0.7002, overlap = 2.246e+04  
steps = 76, shift = 0.14, angle = 0.136 degrees  
  
Position of S2b.map (#3) relative to s2a.map (#2) coordinates:  
Matrix rotation and translation  
0.99999893 0.00046750 0.00138637 -0.48017172  
-0.00047010 0.99999813 0.00187416 -0.36067376  
-0.00138549 -0.00187481 0.99999728 0.77296866  
Axis -0.78830302 0.58284662 -0.19715010  
Axis point 0.00000000 413.67917942 197.80659664  
Rotation angle (degrees) 0.13624199  
Shift along axis 0.01591248  
  

> fitmap #4 inMap #2

Fit map S2c.map in map s2a.map using 136539 points  
correlation = 0.8642, correlation about mean = 0.7029, overlap = 1.999e+04  
steps = 104, shift = 0.159, angle = 0.164 degrees  
  
Position of S2c.map (#4) relative to s2a.map (#2) coordinates:  
Matrix rotation and translation  
0.99999665 -0.00085462 0.00244505 -0.42250571  
0.00085166 0.99999890 0.00121219 -0.51096848  
-0.00244609 -0.00121011 0.99999628 0.87778449  
Axis -0.42358399 0.85530631 0.29837514  
Axis point 358.12126580 0.00000000 172.62607561  
Rotation angle (degrees) 0.16382554  
Shift along axis 0.00384116  
  

> fitmap #5 inMap #2

Fit map S2d.map in map s2a.map using 79890 points  
correlation = 0.9046, correlation about mean = 0.6581, overlap = 1.853e+04  
steps = 64, shift = 0.137, angle = 0.13 degrees  
  
Position of S2d.map (#5) relative to s2a.map (#2) coordinates:  
Matrix rotation and translation  
0.99999863 0.00027462 0.00163284 -0.48201429  
-0.00027715 0.99999876 0.00155123 -0.31736122  
-0.00163241 -0.00155168 0.99999746 0.76429665  
Axis -0.68374678 0.71951844 -0.12158762  
Axis point 468.36598992 0.00000000 292.11829933  
Rotation angle (degrees) 0.13000708  
Shift along axis 0.00829947  
  

> fitmap #6 inMap #2

Fit map S2e.map in map s2a.map using 79966 points  
correlation = 0.9225, correlation about mean = 0.5942, overlap = 1.213e+04  
steps = 36, shift = 0.0474, angle = 0.0524 degrees  
  
Position of S2e.map (#6) relative to s2a.map (#2) coordinates:  
Matrix rotation and translation  
0.99999959 -0.00059609 0.00068859 -0.04583687  
0.00059603 0.99999982 0.00008012 -0.17163671  
-0.00068863 -0.00007971 0.99999976 0.17304490  
Axis -0.08741239 0.75319408 0.65196454  
Axis point 263.05002421 0.00000000 68.30544170  
Rotation angle (degrees) 0.05238292  
Shift along axis -0.01244990  
  

> fitmap #7 inMap #2

Fit map S2f.map in map s2a.map using 79936 points  
correlation = 0.9348, correlation about mean = 0.6876, overlap = 1.07e+04  
steps = 48, shift = 0.0304, angle = 0.0769 degrees  
  
Position of S2f.map (#7) relative to s2a.map (#2) coordinates:  
Matrix rotation and translation  
0.99999916 -0.00084681 0.00098555 -0.06122969  
0.00084714 0.99999958 -0.00033593 -0.14685155  
-0.00098527 0.00033677 0.99999946 0.17922134  
Axis 0.25059275 0.73416968 0.63102944  
Axis point 188.31364750 0.00000000 59.72966796  
Rotation angle (degrees) 0.07690306  
Shift along axis -0.01006373  
  

> morph #2-7

Require at least 2 structures for morph  

> morph #2,3,4,5,6,7

Require at least 2 structures for morph  

> morph #2,7

Require at least 2 structures for morph  

> morph #2-7

Require at least 2 structures for morph  

> morph #2 \- #7

Expected a keyword  

> morph #2,#7

Missing or invalid ""structures"" argument: only initial part ""#2"" of atom
specifier valid  

> morph #2-7

Require at least 2 structures for morph  

> morph #2

Require at least 2 structures for morph  

> show #!8.1 models

> volume #8.1 level 0.4249

> save /Users/haandrew/Desktop/image165.png supersample 3

> volume #8.2 level 1.13

> hide #!8.2 models

> volume #8.1 level 0.255

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!3 models

> volume #3 level 0.8318

> volume #3 level 0.4964

> volume #3 level 0.389

> volume #3 level -0.04027

> volume #3 level 0.1744

> hide #!8.1 models

> show #!8.1 models

> volume #8.1 level 0.5949

> hide #4.1 models

> hide #!3 models

> volume #8.1 level 0.9159

> ui mousemode right ""mark point""

> marker #9 position 258,385.2,290.9 color yellow radius 1

> ui mousemode right ""mark point""

> marker #9 position 331.1,315.9,301.1 color yellow radius 1

> ui mousemode right ""mark point""

> marker #9 position 332.2,317,297.5 color yellow radius 1

> hide #9 target m

> close #9

> marker #9 position 256.8,383.9,287.7 color yellow radius 5

> marker change #9 color #d783ff

> marker #9 position 332.3,301.8,314.7 color #d783ff radius 5

> volume #8.2 level 1.07

> hide #!8.2 models

> volume #8.1 level 0.255

> marker #9 position 282.7,424.7,385.4 color #d783ff radius 5

> marker #9 position 394.3,321.1,386.7 color #d783ff radius 5

> marker #9 position 399,325.4,392.8 color #d783ff radius 5

> ui mousemode right ""translate selected models""

> view matrix models #9,1,0,0,3.3082,0,1,0,-2.3625,0,0,1,0.45069

> ui mousemode right ""translate selected models""

> ui mousemode right ""move picked models""

> select add #9

5 atoms, 5 residues, 1 model selected  

> select subtract #9

Nothing selected  

> show #!4 models

> hide #!4 models

> volume #8.1 level 0.4123

> morph #2

Require at least 2 structures for morph  

> show #!2 models

> volume #2 level 0.0432

> volume #2 level 0.1161

> volume #2 level 0.1621

> hide #!2 models

> show #!3 models

> flip vol #8.1

Unknown command: flip vol #8.1  

> volume flip #8.1

Opened cryosparc_P1_J49_001_volume_map.mrc z flip as #10, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> hide #!8 models

> select add #10

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,-0.47129,-0.87055,-0.14151,591.44,-0.4595,0.3793,-0.80311,459.48,0.75283,-0.31348,-0.57878,306.17

> view matrix models
> #10,-0.80294,-0.59076,-0.079295,591.72,0.0014269,0.13113,-0.99136,450.75,0.59606,-0.79612,-0.10444,342.77

> view matrix models
> #10,-0.91107,-0.36137,-0.19838,591.62,0.17443,0.098105,-0.97977,418.36,0.37353,-0.92725,-0.026347,401.35

> volume #10 level 0.941

> volume #3 level 0.6506

> view matrix models
> #10,0.28057,-0.9398,0.19506,371,0.73095,0.077498,-0.67801,235.9,0.62208,0.33281,0.7087,-84.161

> view matrix models
> #10,0.58555,-0.7054,0.39943,209.25,0.80357,0.44016,-0.40067,81.923,0.10682,0.55558,0.82457,-43.722

> view matrix models
> #10,-0.13948,0.35124,0.92584,27.057,0.46669,-0.80131,0.37431,261.3,0.87336,0.48428,-0.052156,-10.494

> view matrix models
> #10,-0.39737,0.88593,0.23922,113.78,-0.50672,-0.42917,0.7477,315.4,0.76507,0.1759,0.61946,-62.535

> view matrix models
> #10,0.12655,0.75686,0.64121,-59.24,-0.8182,-0.28583,0.49885,405.86,0.56084,-0.58777,0.58309,156.41

> hide #!3 models

> view matrix models
> #10,0.79724,-0.39763,0.4542,83.944,0.0095689,0.76064,0.6491,-36.323,-0.60358,-0.51315,0.61022,391.09

> view matrix models
> #10,0.16855,-0.93043,0.32542,365.9,0.84088,0.30798,0.44504,-77.634,-0.5143,0.19863,0.83429,168.81

> view matrix models
> #10,0.19504,-0.7426,0.6407,252.05,0.72108,0.55137,0.41956,-98.759,-0.66483,0.38017,0.64302,203.22

> show #!3 models

> show #!2 models

> volume #2 level 0.3039

> volume #2 level 0.3614

> view matrix models
> #10,0.19167,-0.75748,0.62408,259.57,0.73621,0.53147,0.41896,-97.637,-0.64904,0.37915,0.65954,196.44

> hide #!3 models

> hide #!10 models

> select subtract #10

Nothing selected  

> show #!10 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!1 models

> volume #1 level 0.4227

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> volume #10 level 0.3871

> surface dust #10 size 33.2

> show #!2 models

> volume #2 level 0.2579

> select add #2

2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #2,1,0,0,8.516,0,1,0,-10.038,0,0,1,4.9371

> hide #!2 models

> show #!2 models

> select subtract #2

Nothing selected  

> hide #!10 models

> show #!8.1 models

> volume #8.1 level 0.6326

> select add #8.1

2 models selected  

> view matrix models
> #8.1,-0.69926,-0.23398,-0.67549,627.13,0.16945,0.86374,-0.4746,149.85,0.69449,-0.44633,-0.56433,342.11

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04  
steps = 100, shift = 6.13, angle = 0.0502 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69874496 -0.23441198 -0.67587462 617.22239177  
0.16965598 0.86353464 -0.47489449 158.94373547  
0.69496210 -0.44649631 -0.56362108 342.81711010  
Axis 0.01986679 -0.95900921 0.28267765  
Axis point 232.40643829 0.00000000 330.36090992  
Rotation angle (degrees) 134.38014463  
Shift along axis -43.25954537  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04  
steps = 28, shift = 0.021, angle = 0.00272 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69871811 -0.23442448 -0.67589805 617.21079276  
0.16967932 0.86352299 -0.47490734 158.93421769  
0.69498341 -0.44651228 -0.56358216 342.79502680  
Axis 0.01986387 -0.95900497 0.28269224  
Axis point 232.40094538 0.00000000 330.35495830  
Rotation angle (degrees) 134.37797512  
Shift along axis -43.25301703  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04  
steps = 48, shift = 0.027, angle = 0.0111 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69881107 -0.23452123 -0.67576836 617.22758681  
0.16960459 0.86346103 -0.47504667 159.01557909  
0.69490817 -0.44658129 -0.56362025 342.84803927  
Axis 0.01991569 -0.95898833 0.28274501  
Axis point 232.41512574 0.00000000 330.37919949  
Rotation angle (degrees) 134.38571197  
Shift along axis -43.26300177  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4242, overlap = 1.75e+04  
steps = 28, shift = 0.0098, angle = 0.00432 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69881775 -0.23447655 -0.67577696 617.22412990  
0.16959206 0.86349747 -0.47498490 158.99998902  
0.69490452 -0.44653428 -0.56366200 342.85642338  
Axis 0.01990552 -0.95899966 0.28270730  
Axis point 232.41249284 0.00000000 330.37366254  
Rotation angle (degrees) 134.38619219  
Shift along axis -43.26675303  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4242, overlap = 1.75e+04  
steps = 28, shift = 0.0387, angle = 0.00738 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69874430 -0.23446874 -0.67585562 617.20036926  
0.16958276 0.86354210 -0.47490708 158.94804993  
0.69498064 -0.44645207 -0.56363326 342.80268412  
Axis 0.01990659 -0.95901155 0.28266691  
Axis point 232.40326525 0.00000000 330.34801496  
Rotation angle (degrees) 134.38030701  
Shift along axis -43.24768257  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04  
steps = 44, shift = 0.0306, angle = 0.00758 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69881703 -0.23448250 -0.67577564 617.22354689  
0.16959147 0.86349399 -0.47499143 158.99602998  
0.69490539 -0.44653788 -0.56365807 342.84475048  
Axis 0.01990756 -0.95899858 0.28271082  
Axis point 232.41487280 0.00000000 330.36774689  
Rotation angle (degrees) 134.38614530  
Shift along axis -43.26363325  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4242, overlap = 1.75e+04  
steps = 40, shift = 0.0185, angle = 0.0059 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69875684 -0.23445023 -0.67584908 617.20999385  
0.16962641 0.86352141 -0.47492911 158.95405660  
0.69495738 -0.44650182 -0.56362254 342.81418427  
Axis 0.01988751 -0.95900547 0.28268885  
Axis point 232.40471427 0.00000000 330.35644302  
Rotation angle (degrees) 134.38120914  
Shift along axis -43.25328951  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04  
steps = 48, shift = 0.0213, angle = 0.00687 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69880573 -0.23451361 -0.67577653 617.22504373  
0.16959431 0.86347540 -0.47502422 159.00993871  
0.69491605 -0.44655750 -0.56362938 342.84335997  
Axis 0.01991648 -0.95899261 0.28273044  
Axis point 232.41448747 0.00000000 330.37497003  
Rotation angle (degrees) 134.38528787  
Shift along axis -43.26415339  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4242, overlap = 1.75e+04  
steps = 40, shift = 0.0204, angle = 0.00921 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69874150 -0.23443480 -0.67587029 617.20791351  
0.16962362 0.86354096 -0.47489455 158.94387015  
0.69497349 -0.44647209 -0.56362623 342.80570237  
Axis 0.01988370 -0.95901109 0.28267007  
Axis point 232.40321294 0.00000000 330.35187117  
Rotation angle (degrees) 134.37995827  
Shift along axis -43.25564335  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04  
steps = 48, shift = 0.022, angle = 0.011 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69881149 -0.23453010 -0.67576485 617.22680423  
0.16959863 0.86345844 -0.47505351 159.02083701  
0.69490921 -0.44658164 -0.56361870 342.84747838  
Axis 0.01992025 -0.95898756 0.28274732  
Axis point 232.41522508 0.00000000 330.37970010  
Rotation angle (degrees) 134.38577029  
Shift along axis -43.26448705  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4244, overlap = 1.75e+04  
steps = 28, shift = 0.0299, angle = 0.0112 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69869919 -0.23449606 -0.67589277 617.21237616  
0.16961131 0.86352492 -0.47492812 158.95410121  
0.69501902 -0.44647095 -0.56357098 342.77441915  
Axis 0.01990688 -0.95900516 0.28268854  
Axis point 232.40766096 0.00000000 330.35224728  
Rotation angle (degrees) 134.37669155  
Shift along axis -43.25263287  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04  
steps = 60, shift = 0.0073, angle = 0.00392 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69872462 -0.23443282 -0.67588842 617.20536810  
0.16964807 0.86353427 -0.47489799 158.93413447  
0.69498449 -0.44648609 -0.56360158 342.79735068  
Axis 0.01987585 -0.95900861 0.28267905  
Axis point 232.40042751 0.00000000 330.35137907  
Rotation angle (degrees) 134.37856240  
Shift along axis -43.25009391  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04  
steps = 48, shift = 0.026, angle = 0.00991 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69880627 -0.23451710 -0.67577476 617.22265617  
0.16958919 0.86347600 -0.47502496 159.00958018  
0.69491676 -0.44655452 -0.56363087 342.84207182  
Axis 0.01991911 -0.95899281 0.28272957  
Axis point 232.41399927 0.00000000 330.37347471  
Rotation angle (degrees) 134.38534512  
Shift along axis -43.26292776  
  

> fitmap #3 inMap #2

Fit map S2b.map in map s2a.map using 29082 points  
correlation = 0.9342, correlation about mean = 0.5212, overlap = 1.526e+04  
steps = 128, shift = 14.1, angle = 0.0654 degrees  
  
Position of S2b.map (#3) relative to s2a.map (#2) coordinates:  
Matrix rotation and translation  
0.99999674 0.00072788 0.00244726 -0.79686476  
-0.00073327 0.99999730 0.00220317 -0.36408256  
-0.00244565 -0.00220495 0.99999458 1.12112740  
Axis -0.65345277 0.72531714 -0.21659761  
Axis point 458.92492000 0.00000000 322.54051248  
Rotation angle (degrees) 0.19325574  
Shift along axis 0.01380465  
  

> hide #!8.1 models

> hide #9 models

> hide #!8 models

> close #10

> show #!3 models

> volume #3 level 0.322

> hide #!3 models

> show #!4 models

> volume #4 level 0.1096

> volume #4 level 0.1415

> select add #4

4 models selected  

> view matrix models
> #4,1,-0.00085462,0.0024451,7.9102,0.00085166,1,0.0012122,-8.7285,-0.0024461,-0.0012101,1,2.4362,#8.1,-0.69881,-0.23452,-0.67577,634.07,0.16959,0.86348,-0.47502,140.75,0.69492,-0.44655,-0.56363,349.34

> fitmap #4 inMap #2

Fit map S2c.map in map s2a.map using 265934 points  
correlation = 0.8025, correlation about mean = 0.7438, overlap = 2.071e+04  
steps = 80, shift = 3.86, angle = 0.0102 degrees  
  
Position of S2c.map (#4) relative to s2a.map (#2) coordinates:  
Matrix rotation and translation  
0.99999700 -0.00080964 0.00231071 -0.39889512  
0.00080709 0.99999906 0.00110393 -0.47734111  
-0.00231160 -0.00110206 0.99999672 0.82316809  
Axis -0.41073484 0.86062944 0.30102136  
Axis point 355.75185755 0.00000000 172.94533004  
Rotation angle (degrees) 0.15386339  
Shift along axis 0.00081750  
  

> volume #4 level 0.2264

> select subtract #4

2 models selected  

> hide #!4 models

> show #!5 models

> select add #5

4 models selected  

> view matrix models
> #5,1,0.00027462,0.0016328,9.8966,-0.00027715,1,0.0015512,-8.9945,-0.0016324,-0.0015517,1,3.5357,#8.1,-0.69881,-0.23452,-0.67577,644.45,0.16959,0.86348,-0.47502,132.08,0.69492,-0.44655,-0.56363,352.11

> fitmap #5 inMap #2

Fit map S2d.map in map s2a.map using 79890 points  
correlation = 0.9045, correlation about mean = 0.6579, overlap = 1.854e+04  
steps = 88, shift = 3.17, angle = 0.00302 degrees  
  
Position of S2d.map (#5) relative to s2a.map (#2) coordinates:  
Matrix rotation and translation  
0.99999870 0.00024279 0.00159655 -0.46901772  
-0.00024523 0.99999880 0.00152998 -0.31838440  
-0.00159618 -0.00153037 0.99999756 0.75063976  
Axis -0.68780695 0.71755925 -0.10968282  
Axis point 470.64161925 0.00000000 289.06952343  
Rotation angle (degrees) 0.12746682  
Shift along axis 0.01180168  
  

> hide #!5 models

> select subtract #5

2 models selected  

> show #!6 models

> select add #6

4 models selected  

> view matrix models
> #6,1,-0.00059609,0.00068859,8.8296,0.00059603,1,8.0122e-05,-7.5921,-0.00068863,-7.9712e-05,1,2.5431,#8.1,-0.69881,-0.23452,-0.67577,653.33,0.16959,0.86348,-0.47502,124.66,0.69492,-0.44655,-0.56363,354.48

> fitmap #6 inMap #2

Fit map S2e.map in map s2a.map using 79966 points  
correlation = 0.9224, correlation about mean = 0.594, overlap = 1.214e+04  
steps = 60, shift = 3.69, angle = 0.00453 degrees  
  
Position of S2e.map (#6) relative to s2a.map (#2) coordinates:  
Matrix rotation and translation  
0.99999960 -0.00052817 0.00071763 -0.07258225  
0.00052813 0.99999986 0.00005189 -0.14841263  
-0.00071766 -0.00005151 0.99999974 0.17218540  
Axis -0.05792234 0.80404761 0.59173680  
Axis point 250.80493083 0.00000000 102.34858623  
Rotation angle (degrees) 0.05113884  
Shift along axis -0.01323824  
  

> select subtract #6

2 models selected  

> hide #!6 models

> show #!7 models

> select add #7

4 models selected  

> view matrix models
> #7,1,-0.00084681,0.00098555,8.574,0.00084714,1,-0.00033593,-7.3665,-0.00098527,0.00033677,1,2.4851,#8.1,-0.69881,-0.23452,-0.67577,661.96,0.16959,0.86348,-0.47502,117.44,0.69492,-0.44655,-0.56363,356.79

> fitmap #7 inMap #2

Fit map S2f.map in map s2a.map using 79936 points  
correlation = 0.9349, correlation about mean = 0.6881, overlap = 1.07e+04  
steps = 56, shift = 3.85, angle = 0.00333 degrees  
  
Position of S2f.map (#7) relative to s2a.map (#2) coordinates:  
Matrix rotation and translation  
0.99999912 -0.00090202 0.00096907 -0.04311830  
0.00090235 0.99999953 -0.00034387 -0.13683604  
-0.00096876 0.00034475 0.99999947 0.17988426  
Axis 0.25169858 0.70829650 0.65951793  
Axis point 178.26385524 0.00000000 47.47744818  
Rotation angle (degrees) 0.07837767  
Shift along axis 0.01086359  
  

> select subtract #8.1

2 models selected  

> select subtract #7

Nothing selected  

> hide #!7 models

> show #!8.1 models

> show #9 models

> select add #8.1

2 models selected  

> view matrix models
> #8.1,-0.69881,-0.23452,-0.67577,637.6,0.16959,0.86348,-0.47502,156.18,0.69492,-0.44655,-0.56363,344.02

> view matrix models
> #8.1,-0.69881,-0.23452,-0.67577,625.48,0.16959,0.86348,-0.47502,150.06,0.69492,-0.44655,-0.56363,348.14

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points  
correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04  
steps = 68, shift = 1.17, angle = 0.00408 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69876795 -0.23456240 -0.67579866 617.22993942  
0.16955256 0.86348500 -0.47502167 159.01545354  
0.69496423 -0.44651331 -0.56360498 342.81525378  
Axis 0.01994464 -0.95899467 0.28272147  
Axis point 232.42031979 0.00000000 330.37150411  
Rotation angle (degrees) 134.38241052  
Shift along axis -43.26331539  
  

> select subtract #8.1

Nothing selected  

> hide #!2 models

> show #!3 models

> volume #3 level 0.2951

> volume #3 level 0.2482

> hide #!3 models

> show #!4 models

> show #!5 models

> hide #!4 models

> hide #!5 models

> show #!6 models

> volume #6 level 0.1712

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> open /Users/haandrew/Downloads/8BN3.cif

Summary of feedback from opening /Users/haandrew/Downloads/8BN3.cif  
---  
note | Fetching CCD K from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/K/K.cif  
  
8BN3.cif title:  
Yeast 80S, ES7s delta, eIF5A, Stm1 containing [more info...]  
  
Chain information for 8BN3.cif #10  
---  
Chain | Description | UniProt  
1 | 25S ribosomal RNA |   
2 | 18S ribosomal RNA |   
3 | 5S ribosomal RNA |   
4 | 5.8S ribosomal RNA |   
B | 60S ribosomal protein L1-A | RL1A_YEAST 1-217  
C0 | Small ribosomal subunit protein eS10A | RS10A_YEAST 1-96  
C1 | Small ribosomal subunit protein uS17A | RS11A_YEAST 2-156  
C3 | 40S ribosomal protein S13 | RS13_YEAST 2-151  
C4 | 40S ribosomal protein S14-B | RS14B_YEAST 11-137  
C5 | RPS15 isoform 1 | A0A6A5Q6F2_YEASX 8-131  
C6 | 40S ribosomal protein S16-A | RS16A_YEAST 3-143  
C7 | ES17 | A0A0J9X224_LACKL 2-126  
C8 | 40S ribosomal protein S18-A | RS18A_YEAST 2-146  
C9 | 40S ribosomal protein S19-A | RS19A_YEAST 2-144  
D0 | RPS20 isoform 1 | A0A6A5PVE9_YEASX 15-121  
D1 | Small ribosomal subunit protein eS21A | RS21A_YEAST 1-87  
D2 | RPS22A isoform 1 | A0A6A5PSE9_YEASX 2-130  
D3 | 40S ribosomal protein S23-A | RS23A_YEAST 2-145  
D4 | 40S ribosomal protein S24-A | RS24A_YEAST 2-135  
D5 | 40S ribosomal protein S25 | A0A6A5PZ18_YEASX 36-105  
D6 | RPS26B isoform 1 | A0A6A5Q0E8_YEASX 2-98  
D7 | 40S ribosomal protein S27-A | RS27A_YEAST 2-82  
D8 | RPS28A isoform 1 | A0A6A5Q700_YEASX 5-67  
D9 | RPS29A isoform 1 | A0A6A5PV92_YEASX 4-56  
E0 | 40S ribosomal protein S30-A | RS30A_YEAST 2-61  
E1 | RPS31 isoform 1 | A0A6A5PU37_YEASX 82-152  
L2 | 60S ribosomal protein L2-A | RL2A_YEAST 2-253  
L3 | 60S ribosomal protein L3 | A0A6A5Q627_YEASX 2-387  
L4 | RPL4A isoform 1 | A0A6A5Q3W0_YEASX 2-362  
L5 | RPL5 isoform 1 | A0A6A5Q0W8_YEASX -2-296  
L6 | 60S ribosomal protein L6-A |   
L7 | 60S ribosomal protein L7-A | RL7A_YEAST 23-244  
L8 | 60S ribosomal protein L8-A | RL8A_YEAST 24-256  
L9 | RPL9A isoform 1 | A0A8H4FCT7_YEASX 1-189  
M0 | RPL10 isoform 1 | A0A6A5PUZ5_YEASX 2-219  
M1 | RPL11B isoform 1 | A0A6A5PYM2_YEASX 6-173  
M3 | 60S ribosomal protein L13-A | RL13A_YEAST 2-194  
M4 | 60S ribosomal protein L14-A | RL14A_YEAST 3-138  
M5 | Ribosomal protein L15 | A0A8H4BX09_YEASX 2-203  
M6 | 60S ribosomal protein L16-A | RL16A_YEAST 3-199  
M7 | 60S ribosomal protein L17-A | RL17A_YEAST 2-184  
M8 | 60S ribosomal protein L18-A | RL18A_YEAST 2-186  
M9 | 60S ribosomal protein L19-A | RL19A_YEAST 2-189  
N0 | 60S ribosomal protein L20-A | RL20A_YEAST 1-172  
N1 | 60S ribosomal protein L21-A | RL21A_YEAST 2-160  
N2 | 60S ribosomal protein L22-A | RL22A_YEAST 9-108  
N3 | 60S ribosomal protein L23-A | RL23A_YEAST 2-137  
N4 | RPL24A isoform 1 | A0A6A5PY83_YEASX 1-98  
N5 | 60S ribosomal protein L25 | RL25_YEAST 22-142  
N6 | Large ribosomal subunit protein uL24A | RL26A_YEAST 2-127  
N7 | 60S ribosomal protein L27-A | RL27A_YEAST 2-136  
N8 | 60S ribosomal protein L28 | RL28_YEAST 2-149  
N9 | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 2-57  
O0 | 60S ribosomal protein L30 | RL30_YEAST 9-105  
O1 | 60S ribosomal protein L31-A | RL31A_YEAST 4-112  
O2 | RPL32 isoform 1 | A0A6A5Q1M9_YEASX 2-128  
O3 | 60S ribosomal protein L33-A | RL33A_YEAST 2-107  
O4 | Large ribosomal subunit protein eL34A | RL34A_YEAST 2-112  
O5 | 60S ribosomal protein L35-A | RL35A_YEAST 2-120  
O6 | 60S ribosomal protein L36-A | RL36A_YEAST 2-100  
O7 | Large ribosomal subunit protein eL37A | RL37A_YEAST 2-87  
O8 | RPL38 isoform 1 | A0A6A5PUL8_YEASX 2-78  
O9 | 60S ribosomal protein L39 | RL39_YEAST 2-51  
P | 60S ribosomal protein L41-A |   
Q0 | 60S ribosomal protein L40-A | RL40A_YEAST 77-128  
Q1 | Large ribosomal subunit protein eL41B | RL41B_YEAST 1-25  
Q2 | 60S ribosomal protein L42-A | RL44A_YEAST 2-106  
Q3 | 60S ribosomal protein L43-A | RL43A_YEAST 2-92  
S0 | Small ribosomal subunit protein uS2A | RSSA1_YEAST 2-252  
S1 | Small ribosomal subunit protein eS1 | A0A6A5PRY4_YEASX 20-233  
S2 | RPS2 isoform 1 | A0A6A5PWF7_YEASX 34-250  
S3 | 40S ribosomal protein S3 | A0A6A5Q3Q1_YEASX 3-225  
S4 | Small ribosomal subunit protein eS4A | RS4A_YEAST 2-261  
S5 | Rps5p | A0A1L4AA68_YEASX 20-225  
S6 | Small ribosomal subunit protein eS6A | RS6A_YEAST 1-226  
S7 | 40S ribosomal protein S7-A | RS7A_YEAST 4-187  
S8 | 40S ribosomal protein S8 | A0A0J9X221_LACKL 2-200  
S9 | Small ribosomal subunit protein uS4A | RS9A_YEAST 2-186  
SM | STM1 isoform 1 | A0A8H4FBL9_YEASX 21-138  
SR | Small ribosomal subunit protein RACK1 | GBLP_YEAST 2-319  
eI | Eukaryotic translation initiation factor 5A | A0A8H8ULI0_YEASX 10-154  
  
Non-standard residues in 8BN3.cif #10  
---  
3HE —
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione  
5CT — Hypusine (N~6~-[(2S)-4-amino-2-hydroxybutyl]-L-lysine)  
K — potassium ion  
MG — magnesium ion  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
ZN — zinc ion  
  
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select add #10

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 4 models
selected  

> view matrix models #10,1,0,0,-192.67,0,1,0,69.056,0,0,1,24.732

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,0.30897,0.92926,0.20252,-263.15,-0.65178,0.051814,0.75664,212.71,0.69262,-0.36578,0.62168,30.24

> view matrix models
> #10,-0.40273,0.80951,-0.4272,13.021,-0.86332,-0.18088,0.47112,348.07,0.3041,0.55855,0.77172,-86.494

> view matrix models
> #10,0.21937,0.97326,0.068145,-228.13,-0.57385,0.1852,-0.79774,472.75,-0.78903,0.13589,0.59913,227

> view matrix models
> #10,0.91604,0.40069,-0.017607,-243.39,-0.22757,0.4831,-0.84548,364.44,-0.33027,0.7785,0.53372,40.634

> view matrix models
> #10,0.96208,0.18482,0.20059,-256.23,0.25178,-0.31897,-0.91371,426.98,-0.10489,0.92957,-0.35341,141.77

> view matrix models
> #10,0.27794,0.6918,0.66646,-304.79,-0.1769,-0.64506,0.74337,247.18,0.94417,-0.32451,-0.056911,105.62

> view matrix models
> #10,0.05857,0.91413,0.40117,-251.28,-0.63838,-0.27466,0.71905,274.39,0.76749,-0.29822,0.56747,14.687

> ui mousemode right ""translate selected models""

> view matrix models
> #10,0.05857,0.91413,0.40117,-255,-0.63838,-0.27466,0.71905,319.24,0.76749,-0.29822,0.56747,29.955

> view matrix models
> #10,0.05857,0.91413,0.40117,8.6081,-0.63838,-0.27466,0.71905,349.16,0.76749,-0.29822,0.56747,-38.273

> view matrix models
> #10,0.05857,0.91413,0.40117,-3.1339,-0.63838,-0.27466,0.71905,314.81,0.76749,-0.29822,0.56747,84.619

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,0.20197,0.56316,0.80128,-45.679,-0.70248,-0.48679,0.51919,402.28,0.68245,-0.66775,0.29729,217.02

> ui mousemode right ""translate selected models""

> view matrix models
> #10,0.20197,0.56316,0.80128,-20.057,-0.70248,-0.48679,0.51919,401.18,0.68245,-0.66775,0.29729,214.26

> view matrix models
> #10,0.20197,0.56316,0.80128,-198.99,-0.70248,-0.48679,0.51919,531.3,0.68245,-0.66775,0.29729,409.01

> view matrix models
> #10,0.20197,0.56316,0.80128,-16.643,-0.70248,-0.48679,0.51919,355.78,0.68245,-0.66775,0.29729,323.43

> view matrix models
> #10,0.20197,0.56316,0.80128,-13.859,-0.70248,-0.48679,0.51919,408.36,0.68245,-0.66775,0.29729,234.87

> fitmap #10 inMap #8.1

Fit molecule 8BN3.cif (#10) to map cryosparc_P1_J49_001_volume_map.mrc (#8.1)
using 201660 atoms  
average map value = 0.7505, steps = 180  
shifted from previous position = 16  
rotated from previous position = 39.3 degrees  
atoms outside contour = 70556, contour level = 0.63262  
  
Position of 8BN3.cif (#10) relative to cryosparc_P1_J49_001_volume_map.mrc
(#8.1) coordinates:  
Matrix rotation and translation  
0.65613488 -0.74028800 0.14649469 202.25922708  
-0.72999412 -0.67183893 -0.12546326 501.80546349  
0.19129978 -0.02461944 -0.98122284 361.48342205  
Axis 0.90990948 -0.40427443 0.09288126  
Axis point 0.00000000 290.34778333 178.15544695  
Rotation angle (degrees) 176.82337291  
Shift along axis 14.74550438  
  

> view matrix models
> #10,-0.41654,0.69152,0.59017,175.18,-0.60996,-0.69395,0.38261,414.4,0.67412,-0.20061,0.71085,58.581

> ui mousemode right ""translate selected models""

> select subtract #10

Nothing selected  

> sequence chain #10/SM

Alignment identifier is 10/SM  

> select #10/SM:21

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #10/SM

893 atoms, 903 bonds, 118 residues, 1 model selected  

> color sel red

> sel~sel

Unknown command: sel~sel  

> select ~sel

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 24 models
selected  

> select subtract #1

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 22 models
selected  

> select subtract #2

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 20 models
selected  

> select subtract #3

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 18 models
selected  

> select subtract #4

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 16 models
selected  

> select subtract #5

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 14 models
selected  

> select subtract #6

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 12 models
selected  

> select subtract #7

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 10 models
selected  

> select subtract #8

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 5 models
selected  

> select add #8.1

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 7 models
selected  

> select add #8

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 10 models
selected  

> select subtract #8

200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 5 models
selected  

> select subtract #9

200767 atoms, 213303 bonds, 6055 pseudobonds, 18425 residues, 4 models
selected  

> hide (#!10 & sel) target a

> ~select

Nothing selected  

> hide #!8 models

> show #!8 models

> hide #9 models

> volume #8.1 level 0.3242

> ui tool show ""Side View""

> volume #8.1 level 0.8277

> volume #8.1 level 0.1794

> open /Users/haandrew/Documents/progress/2025/Cryo-
> EM/20250506_scRibso_SND1/maps/apo_cryosparc_P2_J306_004_volume_map_sharp.mrc

Opened apo_cryosparc_P2_J306_004_volume_map_sharp.mrc as #11, grid size
400,400,400, pixel 0.86, shown at level 0.214, step 2, values float32  

> volume #11 level 0.2598

> select add #11

3 models selected  

> view matrix models #11,1,0,0,-108.12,0,1,0,44.884,0,0,1,6.4872

> volume #11 level 0.4262

> select subtract #11

Nothing selected  

> close #11

> open /Users/haandrew/Documents/progress/2025/Cryo-
> EM/20250506_scRibso_SND1/maps/cryosparc_P1_J25_mask.mrc

Opened cryosparc_P1_J25_mask.mrc as #11, grid size 128,128,128, pixel 3.35,
shown at level 5e-05, step 1, values float32  

> select add #11

2 models selected  

> close #11

> open /Users/haandrew/Documents/progress/2025/Cryo-
> EM/20250506_scRibso_SND1/maps/apo_cryosparc_P2_J306_004_volume_map_sharp.mrc

Opened apo_cryosparc_P2_J306_004_volume_map_sharp.mrc as #11, grid size
400,400,400, pixel 0.86, shown at level 0.214, step 2, values float32  

> select add #11

3 models selected  

> view matrix models #11,1,0,0,-101.94,0,1,0,-61.742,0,0,1,66.111

> volume #11 level -0.3903

> close #11

> open /Users/haandrew/Documents/progress/2025/Cryo-
> EM/20250506_scRibso_SND1/maps/NU_cryosparc_P1_J23_002_volume_map_sharp.mrc

Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc as #11, grid size
128,128,128, pixel 3.35, shown at level 1.87, step 1, values float32  

> select add #11

2 models selected  

> view matrix models #11,1,0,0,-62.35,0,1,0,-108.99,0,0,1,88.193

> view matrix models #11,1,0,0,-80.234,0,1,0,-139.87,0,0,1,104.88

> volume #11 level 0.5448

> ui mousemode right ""rotate selected models""

> view matrix models
> #11,-0.77355,-0.26162,0.57722,257.19,-0.18669,-0.77633,-0.60205,415.96,0.60562,-0.57347,0.55169,186.86

> view matrix models
> #11,-0.79278,0.50799,0.33681,148.41,-0.5134,-0.85439,0.080198,359.22,0.32851,-0.10934,0.93815,66.506

> ui mousemode right ""translate selected models""

> view matrix models
> #11,-0.79278,0.50799,0.33681,99.56,-0.5134,-0.85439,0.080198,303.42,0.32851,-0.10934,0.93815,75.073

> volume #11 level 1.757

> ui mousemode right ""rotate selected models""

> view matrix models
> #11,-0.28671,0.83043,-0.47769,97.568,-0.47714,0.30861,0.82286,-106.26,0.83074,0.46385,0.30775,-17.872

> view matrix models
> #11,-0.24518,0.96618,0.079905,-58.11,0.95394,0.22573,0.19759,-259.09,0.17287,0.12467,-0.97702,465.39

> show #9 models

> ui mousemode right ""translate selected models""

> view matrix models
> #11,-0.24518,0.96618,0.079905,-19.501,0.95394,0.22573,0.19759,-191.18,0.17287,0.12467,-0.97702,238.18

> ui mousemode right ""rotate selected models""

> view matrix models
> #11,-0.44466,0.86193,0.24364,9.8808,0.43509,0.44561,-0.78238,80.482,-0.78293,-0.24189,-0.57316,431.83

> view matrix models
> #11,-0.18798,0.93156,-0.31122,58.69,-0.76591,-0.3374,-0.54731,449.37,-0.61485,0.13548,0.77692,30.371

> view matrix models
> #11,0.33453,0.89427,0.29728,-173.26,-0.90067,0.21057,0.38008,165.9,0.27729,-0.3949,0.87588,-68.074

> view matrix models
> #11,-0.023396,0.72365,0.68977,-144.95,-0.75877,-0.4621,0.45906,260.43,0.65094,-0.51264,0.5599,-55.367

> select add #8.1

5 models selected  

> select subtract #8.1

2 models selected  

> volume #8.1 level 0.8214

> view matrix models
> #11,-0.25849,0.86303,0.434,-70.173,-0.92617,-0.34911,0.14259,339.31,0.27457,-0.3651,0.88956,-76.664

> view matrix models
> #11,-0.2556,0.76987,0.58479,-83.218,-0.66743,-0.57812,0.46937,263.28,0.69943,-0.27033,0.6616,-138.13

> ui mousemode right ""translate selected models""

> view matrix models
> #11,-0.2556,0.76987,0.58479,37.46,-0.66743,-0.57812,0.46937,405.92,0.69943,-0.27033,0.6616,74.829

> view matrix models
> #11,-0.2556,0.76987,0.58479,-61.132,-0.66743,-0.57812,0.46937,246.04,0.69943,-0.27033,0.6616,168.26

> vlo flip #11

Unknown command: vlo flip #11  

> volume flip #11

Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc z flip as #12, grid size
128,128,128, pixel 3.35, shown at step 1, values float32  

> select subtract #11

Nothing selected  

> select add #12

2 models selected  

> view matrix models
> #12,-0.2556,0.76987,0.58479,-43.002,-0.66743,-0.57812,0.46937,298.27,0.69943,-0.27033,0.6616,-194.26

> ui mousemode right ""rotate selected models""

> view matrix models
> #12,0.92577,0.31188,-0.21375,-26.853,0.27852,-0.94484,-0.17233,311.69,-0.25571,0.10001,-0.96157,275.75

> view matrix models
> #12,0.62393,0.48527,-0.61256,85.536,0.17958,-0.8519,-0.49196,381.16,-0.76057,0.19695,-0.61866,289.25

> ui mousemode right ""translate selected models""

> view matrix models
> #12,0.62393,0.48527,-0.61256,188.72,0.17958,-0.8519,-0.49196,497.09,-0.76057,0.19695,-0.61866,541.82

> fitmap #11 inMap #8.1

Fit map NU_cryosparc_P1_J23_002_volume_map_sharp.mrc in map
cryosparc_P1_J49_001_volume_map.mrc using 23893 points  
correlation = 0.01935, correlation about mean = -0.01646, overlap = 1.348  
steps = 2000, shift = 45.8, angle = 16.9 degrees  
  
Position of NU_cryosparc_P1_J23_002_volume_map_sharp.mrc (#11) relative to
cryosparc_P1_J49_001_volume_map.mrc (#8.1) coordinates:  
Matrix rotation and translation  
0.76596209 -0.63078757 0.12413352 322.16906811  
-0.63024789 -0.77487124 -0.04860213 313.54152615  
0.12684511 -0.04100750 -0.99107452 517.38272158  
Axis 0.93967044 -0.33550078 0.06677342  
Axis point 0.00000000 213.74492934 247.66543738  
Rotation angle (degrees) 179.76846061  
Shift along axis 232.08674081  
  

> view matrix models
> #12,0.62393,0.48527,-0.61256,175.9,0.17958,-0.8519,-0.49196,515.24,-0.76057,0.19695,-0.61866,538.55

> fitmap #11 inMap #8.1

Fit map NU_cryosparc_P1_J23_002_volume_map_sharp.mrc in map
cryosparc_P1_J49_001_volume_map.mrc using 23893 points  
correlation = 0.02243, correlation about mean = -0.02075, overlap = 1.595  
steps = 2000, shift = 2.98, angle = 1.59 degrees  
  
Position of NU_cryosparc_P1_J23_002_volume_map_sharp.mrc (#11) relative to
cryosparc_P1_J49_001_volume_map.mrc (#8.1) coordinates:  
Matrix rotation and translation  
0.76039117 -0.63772002 0.12295710 323.96547670  
-0.63353104 -0.77000069 -0.07574545 319.50905901  
0.14298144 -0.02030097 -0.98951715 511.69616259  
Axis 0.93817345 -0.33883092 0.07088153  
Axis point 0.00000000 214.35569589 246.74521785  
Rotation angle (degrees) 178.30671110  
Shift along axis 231.94606760  
  

> fitmap #11 inMap #8.1

Fit map NU_cryosparc_P1_J23_002_volume_map_sharp.mrc in map
cryosparc_P1_J49_001_volume_map.mrc using 23893 points  
correlation = 0.02113, correlation about mean = -0.01959, overlap = 1.58  
steps = 2000, shift = 1.67, angle = 0.811 degrees  
  
Position of NU_cryosparc_P1_J23_002_volume_map_sharp.mrc (#11) relative to
cryosparc_P1_J49_001_volume_map.mrc (#8.1) coordinates:  
Matrix rotation and translation  
0.75875117 -0.64007885 0.12081283 325.17547265  
-0.63770232 -0.76773938 -0.06254596 316.26964319  
0.13278712 -0.02958580 -0.99070292 514.78491310  
Axis 0.93774531 -0.34067882 0.06761421  
Axis point 0.00000000 214.86367769 247.52162959  
Rotation angle (degrees) 178.99302339  
Shift along axis 231.99217871  
  

> select subtract #12

Nothing selected  

> volume #8.1 level 0.2738

> volume #11 level 2.705

> fitmap #12 inMap #8.1

Fit map NU_cryosparc_P1_J23_002_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map.mrc using 23893 points  
correlation = 0.9682, correlation about mean = 0.4313, overlap = 5.764e+04  
steps = 76, shift = 6.77, angle = 9.6 degrees  
  
Position of NU_cryosparc_P1_J23_002_volume_map_sharp.mrc z flip (#12) relative
to cryosparc_P1_J49_001_volume_map.mrc (#8.1) coordinates:  
Matrix rotation and translation  
-0.97709476 -0.21259809 -0.00937515 470.84629512  
0.21276995 -0.97519050 -0.06109367 392.99085428  
0.00384584 -0.06168906 0.99808801 9.67927862  
Axis -0.00139902 -0.03106627 0.99951635  
Axis point 214.27703954 221.99548795 0.00000000  
Rotation angle (degrees) 167.71427589  
Shift along axis -3.19288320  
  

> hide #!11 models

> volume #12 level 0.45

> hide #9 models

> hide #!8.1 models

> ui tool show ""Side View""

> volume #7 level 0.04281

> hide #!7 models

> show #!8.1 models

Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py"", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/sideview/tool.py"", line 113, in _redraw  
self.render()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/sideview/tool.py"", line 143, in render  
mvwin = self.view.render.use_shared_context(self)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 579, in use_shared_context  
self.make_current()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 550, in make_current  
return self._opengl_context.make_current()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 123, in make_current  
raise OpenGLError(""Could not make graphics context current"")  
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current  
  
Error processing trigger ""frame drawn"":  
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current  
  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 123, in make_current  
raise OpenGLError(""Could not make graphics context current"")  
  
See log for complete Python traceback.  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #!8 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui tool show ""Side View""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> save ""/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39
> and exit focus mask /NU/scribo comp apo rotat.tif"" width 864 height 590
> supersample 3

> show #!8.2 models

> hide #!8.2 models

> save ""/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39
> and exit focus mask /NU/J49 comp.tif"" width 864 height 587 supersample 3

> close session

Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py"", line 150, in status  
r.draw_background()  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 1220, in draw_background  
GL.glClear(flags)  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File ""src/errorchecker.pyx"", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J103_001_volume_map_sharp.mrc""

Opened cryosparc_P1_J103_001_volume_map_sharp.mrc as #1, grid size
128,128,128, pixel 3.32, shown at level 1.41, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J103_001_volume_map.mrc""

Opened cryosparc_P1_J103_001_volume_map.mrc as #2, grid size 128,128,128,
pixel 3.32, shown at level 1.04, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J104_001_volume_map_sharp.mrc""

Opened cryosparc_P1_J104_001_volume_map_sharp.mrc as #3, grid size
128,128,128, pixel 3.32, shown at level 1.4, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J104_001_volume_map.mrc""

Opened cryosparc_P1_J104_001_volume_map.mrc as #4, grid size 128,128,128,
pixel 3.32, shown at level 1.04, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J108_001_volume_map_sharp.mrc""

Opened cryosparc_P1_J108_001_volume_map_sharp.mrc as #5, grid size
128,128,128, pixel 3.32, shown at level 1.01, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J108_001_volume_map.mrc""

Opened cryosparc_P1_J108_001_volume_map.mrc as #6, grid size 128,128,128,
pixel 3.32, shown at level 0.863, step 1, values float32  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> show #!2 models

> show #!1 models

> volume #1 level 0.4865

> surface dust #1 size 33.2

> surface dust #2 size 33.2

> volume #2 level 0.1316

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!2 models

> open ""/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /100625_allmaps
> overlay w NU 2.cxs""

restore_snapshot for ""Volume"" returned None  

restore_snapshot for ""VolumeSurface"" returned None  

Opened ec8 ribso _ cryosparc_P26_J24_001_volume_map.mrc as #1, grid size
128,128,128, pixel 3.35, shown at level 0.86, step 1, values float32  
Opened cryosparc_P1_J21_class_04_00082_volume.mrc as #2, grid size
128,128,128, pixel 3.32, shown at level 0.34, step 1, values float32  
Opened cryosparc_P1_J21_class_03_00082_volume.mrc as #3, grid size
128,128,128, pixel 3.32, shown at level 0.108, step 1, values float32  
Opened cryosparc_P1_J21_class_02_00082_volume.mrc as #4, grid size
128,128,128, pixel 3.32, shown at level 0.0537, step 1, values float32  
Opened cryosparc_P1_J21_class_01_00082_volume.mrc as #5, grid size
128,128,128, pixel 3.32, shown at level 0.59, step 1, values float32  
Opened cryosparc_P1_J21_class_00_00082_volume.mrc as #6, grid size
128,128,128, pixel 3.32, shown at level 0.249, step 1, values float32  
Opened cryosparc_P1_J21_class_00_00082_volume.mrc z flip as #7, grid size
128,128,128, pixel 3.32, shown at level 0.618, step 1, values float32  
Opened cryosparc_P1_J21_class_01_00082_volume.mrc z flip as #8, grid size
128,128,128, pixel 3.32, shown at level 0.498, step 1, values float32  
Opened cryosparc_P1_J24_001_volume_map.mrc z flip as #10, grid size
128,128,128, pixel 3.32, shown at level -0.0329, step 1, values float32  
Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc as #11, grid size
128,128,128, pixel 3.35, shown at level 0.147, step 1, values float32  
Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc z flip as #12, grid size
128,128,128, pixel 3.35, shown at level 0.223, step 1, values float32  
opened ChimeraX session  

> close session

> open /Users/haandrew/Documents/progress/2025/Cryo-
> EM/20250506_scRibso_SND1/maps/apo_cryosparc_P2_J306_004_volume_map_sharp.mrc
> format mrc

Opened apo_cryosparc_P2_J306_004_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.86, shown at level 0.214, step 2, values float32  

> close session

> open /Users/haandrew/Documents/progress/2026/Cryo-
> EM/2025-09-25/ecsnd40_scribo/cryosparc_P1_J49_001_volume_map_sharp.mrc

Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #1, grid size 128,128,128,
pixel 3.32, shown at level 1.35, step 1, values float32  

> open /Users/haandrew/Documents/progress/2026/Cryo-
> EM/2025-09-25/ecsnd40_scribo/cryosparc_P1_J49_001_volume_map.mrc

Opened cryosparc_P1_J49_001_volume_map.mrc as #2, grid size 128,128,128, pixel
3.32, shown at level 1.03, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J96_ class
> 0/NU refinement /cryosparc_P1_J97_002_volume_map_sharp.mrc""

Opened cryosparc_P1_J97_002_volume_map_sharp.mrc as #3, grid size 128,128,128,
pixel 3.32, shown at level 0.721, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J96_ class
> 0/NU refinement /cryosparc_P1_J97_002_volume_map.mrc""

Opened cryosparc_P1_J97_002_volume_map.mrc as #4, grid size 128,128,128, pixel
3.32, shown at level 0.721, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J96_ class
> 0/NU refinement /cryosparc_P1_J98_001_volume_map_sharp.mrc""

Opened cryosparc_P1_J98_001_volume_map_sharp.mrc as #5, grid size 128,128,128,
pixel 3.32, shown at level 1.11, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J96_ class
> 0/NU refinement /cryosparc_P1_J98_001_volume_map.mrc""

Opened cryosparc_P1_J98_001_volume_map.mrc as #6, grid size 128,128,128, pixel
3.32, shown at level 0.905, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J103_001_volume_map_sharp.mrc""

Opened cryosparc_P1_J103_001_volume_map_sharp.mrc as #7, grid size
128,128,128, pixel 3.32, shown at level 1.41, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J103_001_volume_map.mrc""

Opened cryosparc_P1_J103_001_volume_map.mrc as #8, grid size 128,128,128,
pixel 3.32, shown at level 1.04, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J104_001_volume_map_sharp.mrc""

Opened cryosparc_P1_J104_001_volume_map_sharp.mrc as #9, grid size
128,128,128, pixel 3.32, shown at level 1.4, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J104_001_volume_map.mrc""

Opened cryosparc_P1_J104_001_volume_map.mrc as #10, grid size 128,128,128,
pixel 3.32, shown at level 1.04, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J108_001_volume_map_sharp.mrc""

Opened cryosparc_P1_J108_001_volume_map_sharp.mrc as #11, grid size
128,128,128, pixel 3.32, shown at level 1.01, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
> 1/NU-refinement /cryosparc_P1_J108_001_volume_map.mrc""

Opened cryosparc_P1_J108_001_volume_map.mrc as #12, grid size 128,128,128,
pixel 3.32, shown at level 0.863, step 1, values float32  

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/8BN3.cif""

8BN3.cif title:  
Yeast 80S, ES7s delta, eIF5A, Stm1 containing [more info...]  
  
Chain information for 8BN3.cif #13  
---  
Chain | Description | UniProt  
1 | 25S ribosomal RNA |   
2 | 18S ribosomal RNA |   
3 | 5S ribosomal RNA |   
4 | 5.8S ribosomal RNA |   
B | 60S ribosomal protein L1-A | RL1A_YEAST 1-217  
C0 | Small ribosomal subunit protein eS10A | RS10A_YEAST 1-96  
C1 | Small ribosomal subunit protein uS17A | RS11A_YEAST 2-156  
C3 | 40S ribosomal protein S13 | RS13_YEAST 2-151  
C4 | 40S ribosomal protein S14-B | RS14B_YEAST 11-137  
C5 | RPS15 isoform 1 | A0A6A5Q6F2_YEASX 8-131  
C6 | 40S ribosomal protein S16-A | RS16A_YEAST 3-143  
C7 | ES17 | A0A0J9X224_LACKL 2-126  
C8 | 40S ribosomal protein S18-A | RS18A_YEAST 2-146  
C9 | 40S ribosomal protein S19-A | RS19A_YEAST 2-144  
D0 | RPS20 isoform 1 | A0A6A5PVE9_YEASX 15-121  
D1 | Small ribosomal subunit protein eS21A | RS21A_YEAST 1-87  
D2 | RPS22A isoform 1 | A0A6A5PSE9_YEASX 2-130  
D3 | 40S ribosomal protein S23-A | RS23A_YEAST 2-145  
D4 | 40S ribosomal protein S24-A | RS24A_YEAST 2-135  
D5 | 40S ribosomal protein S25 | A0A6A5PZ18_YEASX 36-105  
D6 | RPS26B isoform 1 | A0A6A5Q0E8_YEASX 2-98  
D7 | 40S ribosomal protein S27-A | RS27A_YEAST 2-82  
D8 | RPS28A isoform 1 | A0A6A5Q700_YEASX 5-67  
D9 | RPS29A isoform 1 | A0A6A5PV92_YEASX 4-56  
E0 | 40S ribosomal protein S30-A | RS30A_YEAST 2-61  
E1 | RPS31 isoform 1 | A0A6A5PU37_YEASX 82-152  
L2 | 60S ribosomal protein L2-A | RL2A_YEAST 2-253  
L3 | 60S ribosomal protein L3 | A0A6A5Q627_YEASX 2-387  
L4 | RPL4A isoform 1 | A0A6A5Q3W0_YEASX 2-362  
L5 | RPL5 isoform 1 | A0A6A5Q0W8_YEASX -2-296  
L6 | 60S ribosomal protein L6-A |   
L7 | 60S ribosomal protein L7-A | RL7A_YEAST 23-244  
L8 | 60S ribosomal protein L8-A | RL8A_YEAST 24-256  
L9 | RPL9A isoform 1 | A0A8H4FCT7_YEASX 1-189  
M0 | RPL10 isoform 1 | A0A6A5PUZ5_YEASX 2-219  
M1 | RPL11B isoform 1 | A0A6A5PYM2_YEASX 6-173  
M3 | 60S ribosomal protein L13-A | RL13A_YEAST 2-194  
M4 | 60S ribosomal protein L14-A | RL14A_YEAST 3-138  
M5 | Ribosomal protein L15 | A0A8H4BX09_YEASX 2-203  
M6 | 60S ribosomal protein L16-A | RL16A_YEAST 3-199  
M7 | 60S ribosomal protein L17-A | RL17A_YEAST 2-184  
M8 | 60S ribosomal protein L18-A | RL18A_YEAST 2-186  
M9 | 60S ribosomal protein L19-A | RL19A_YEAST 2-189  
N0 | 60S ribosomal protein L20-A | RL20A_YEAST 1-172  
N1 | 60S ribosomal protein L21-A | RL21A_YEAST 2-160  
N2 | 60S ribosomal protein L22-A | RL22A_YEAST 9-108  
N3 | 60S ribosomal protein L23-A | RL23A_YEAST 2-137  
N4 | RPL24A isoform 1 | A0A6A5PY83_YEASX 1-98  
N5 | 60S ribosomal protein L25 | RL25_YEAST 22-142  
N6 | Large ribosomal subunit protein uL24A | RL26A_YEAST 2-127  
N7 | 60S ribosomal protein L27-A | RL27A_YEAST 2-136  
N8 | 60S ribosomal protein L28 | RL28_YEAST 2-149  
N9 | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 2-57  
O0 | 60S ribosomal protein L30 | RL30_YEAST 9-105  
O1 | 60S ribosomal protein L31-A | RL31A_YEAST 4-112  
O2 | RPL32 isoform 1 | A0A6A5Q1M9_YEASX 2-128  
O3 | 60S ribosomal protein L33-A | RL33A_YEAST 2-107  
O4 | Large ribosomal subunit protein eL34A | RL34A_YEAST 2-112  
O5 | 60S ribosomal protein L35-A | RL35A_YEAST 2-120  
O6 | 60S ribosomal protein L36-A | RL36A_YEAST 2-100  
O7 | Large ribosomal subunit protein eL37A | RL37A_YEAST 2-87  
O8 | RPL38 isoform 1 | A0A6A5PUL8_YEASX 2-78  
O9 | 60S ribosomal protein L39 | RL39_YEAST 2-51  
P | 60S ribosomal protein L41-A |   
Q0 | 60S ribosomal protein L40-A | RL40A_YEAST 77-128  
Q1 | Large ribosomal subunit protein eL41B | RL41B_YEAST 1-25  
Q2 | 60S ribosomal protein L42-A | RL44A_YEAST 2-106  
Q3 | 60S ribosomal protein L43-A | RL43A_YEAST 2-92  
S0 | Small ribosomal subunit protein uS2A | RSSA1_YEAST 2-252  
S1 | Small ribosomal subunit protein eS1 | A0A6A5PRY4_YEASX 20-233  
S2 | RPS2 isoform 1 | A0A6A5PWF7_YEASX 34-250  
S3 | 40S ribosomal protein S3 | A0A6A5Q3Q1_YEASX 3-225  
S4 | Small ribosomal subunit protein eS4A | RS4A_YEAST 2-261  
S5 | Rps5p | A0A1L4AA68_YEASX 20-225  
S6 | Small ribosomal subunit protein eS6A | RS6A_YEAST 1-226  
S7 | 40S ribosomal protein S7-A | RS7A_YEAST 4-187  
S8 | 40S ribosomal protein S8 | A0A0J9X221_LACKL 2-200  
S9 | Small ribosomal subunit protein uS4A | RS9A_YEAST 2-186  
SM | STM1 isoform 1 | A0A8H4FBL9_YEASX 21-138  
SR | Small ribosomal subunit protein RACK1 | GBLP_YEAST 2-319  
eI | Eukaryotic translation initiation factor 5A | A0A8H8ULI0_YEASX 10-154  
  
Non-standard residues in 8BN3.cif #13  
---  
3HE —
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione  
5CT — Hypusine (N~6~-[(2S)-4-amino-2-hydroxybutyl]-L-lysine)  
K — potassium ion  
MG — magnesium ion  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
ZN — zinc ion  
  
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> select add #1

2 models selected  

> view matrix models #1,1,0,0,-77.885,0,1,0,-82.845,0,0,1,264.99

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.98534,-0.14956,0.082036,364.9,0.15644,-0.60059,0.7841,72.381,-0.067999,0.78544,0.61519,186.94

> view matrix models
> #1,-0.91922,-0.35372,-0.17299,449.03,0.032347,-0.50569,0.86211,61.831,-0.39242,0.78687,0.47628,285.45

> view matrix models
> #1,0.78258,-0.59551,0.18149,62.202,-0.61166,-0.6812,0.40229,335.2,-0.11594,-0.42583,-0.89734,780.65

> view matrix models
> #1,0.60971,-0.76823,0.19512,134.61,-0.79261,-0.5925,0.14392,408.6,0.0050465,-0.2424,-0.97016,729.42

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.60971,-0.76823,0.19512,179.95,-0.79261,-0.5925,0.14392,459.05,0.0050465,-0.2424,-0.97016,453.45

Must specify one map, got 0  

> fitmap #13 inMap #1

Fit molecule 8BN3.cif (#13) to map cryosparc_P1_J49_001_volume_map_sharp.mrc
(#1) using 201660 atoms  
average map value = 0.8785, steps = 100  
shifted from previous position = 12.8  
rotated from previous position = 11.1 degrees  
atoms outside contour = 167040, contour level = 1.3494  
  
Position of 8BN3.cif (#13) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.65584968 -0.74067363 0.14582099 202.50006646  
-0.73031822 -0.67143512 -0.12573852 501.85180835  
0.19104054 -0.02403016 -0.98128796 361.42298213  
Axis 0.90982978 -0.40451043 0.09263410  
Axis point 0.00000000 290.40740866 178.20792008  
Rotation angle (degrees) 176.79583012  
Shift along axis 14.71639185  
  

> hide #!1 models

> show #!1 models

> hide #!13 models

> show #!2 models

> select subtract #1

Nothing selected  

> select add #2

2 models selected  

> view matrix models #2,1,0,0,-196.92,0,1,0,-275.06,0,0,1,20.825

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.84944,0.29244,0.43925,-319.5,0.12244,-0.91891,0.37499,37.095,0.51329,-0.26475,-0.81636,346.19

> view matrix models
> #2,0.09898,-0.8071,0.58206,54.422,0.98403,-0.0075873,-0.17786,-234.39,0.14796,0.59037,0.79346,-96.832

> view matrix models
> #2,0.096664,-0.80131,0.59038,51.928,0.98625,-0.0027749,-0.16525,-238.57,0.13405,0.59824,0.79003,-94.776

> view matrix models
> #2,-0.91463,0.31644,0.25165,101.44,-0.21527,-0.90802,0.35938,112.06,0.34222,0.27453,0.89862,-92.734

> view matrix models
> #2,-0.96898,0.12837,-0.21117,251.19,-0.065215,-0.95704,-0.28253,224.23,-0.23837,-0.25999,0.93573,143.13

> view matrix models
> #2,0.60659,-0.75834,-0.23869,104.35,-0.76626,-0.6377,0.078712,232.85,-0.2119,0.13515,-0.9679,449.96

> view matrix models
> #2,0.63412,-0.75563,-0.16406,82.094,-0.74362,-0.6541,0.13849,218.94,-0.21196,0.034178,-0.97668,473.78

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.63412,-0.75563,-0.16406,53.202,-0.74362,-0.6541,0.13849,244.2,-0.21196,0.034178,-0.97668,471.88

> view matrix models
> #2,0.63412,-0.75563,-0.16406,237.24,-0.74362,-0.6541,0.13849,468.19,-0.21196,0.034178,-0.97668,430.77

> fitmap #2 inMap #1

Fit map cryosparc_P1_J49_001_volume_map.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20953 points  
correlation = 0.9918, correlation about mean = 0.843, overlap = 4.752e+04  
steps = 124, shift = 18.5, angle = 20.8 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#2) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999996 -0.00024974 -0.00020887 0.12635677  
0.00024970 0.99999998 -0.00015085 0.00699286  
0.00020891 0.00015080 0.99999998 -0.10194766  
Axis 0.42036197 -0.58217057 0.69596928  
Axis point 23.16499136 542.83512047 0.00000000  
Rotation angle (degrees) 0.02055816  
Shift along axis -0.02190789  
  

> select subtract #2

Nothing selected  

> hide #!2 models

> select add #3

2 models selected  

> show #!3 models

> view matrix models #3,1,0,0,40.953,0,1,0,-307.01,0,0,1,-5.0511

> volume #3 level 0.3894

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,-0.57638,0.7749,-0.25944,269.35,0.048851,0.34959,0.93563,-390.8,0.81572,0.52661,-0.23935,-9.6521

> view matrix models
> #3,-0.58918,0.71997,-0.36676,307.49,0.027464,0.47149,0.88144,-399.6,0.80753,0.50926,-0.29757,8.7028

> view matrix models
> #3,-0.81182,0.4742,-0.3407,399.82,-0.17891,0.35341,0.9182,-339.73,0.55582,0.80637,-0.20207,-21.592

> hide #!3 models

> show #!4 models

> select subtract #3

Nothing selected  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!5 models

> select add #5

2 models selected  

> view matrix models
> #5,0.96748,0.20643,-0.14617,-4.8407,-0.13708,0.91357,0.38289,-34.846,0.21257,-0.3504,0.91216,46.725

> ui mousemode right ""move picked models""

> view matrix models
> #5,0.96748,0.20643,-0.14617,-9.6451,-0.13708,0.91357,0.38289,-328.73,0.21257,-0.3504,0.91216,19.868

> view matrix models
> #5,0.96748,0.20643,-0.14617,-87.654,-0.13708,0.91357,0.38289,-432.87,0.21257,-0.3504,0.91216,-51.34

> view matrix models
> #5,0.96748,0.20643,-0.14617,-137.77,-0.13708,0.91357,0.38289,-428.28,0.21257,-0.3504,0.91216,-64.854

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,0.91286,0.31669,-0.25766,-125.47,-0.32278,0.94627,0.019499,-319.02,0.24999,0.065367,0.96604,-170.12

> view matrix models
> #5,0.98317,0.18107,0.024322,-172.03,-0.18141,0.98333,0.012507,-354.74,-0.021651,-0.016709,0.99963,-103.52

> view matrix models
> #5,0.88751,-0.45408,0.07828,-32.144,0.46072,0.87174,-0.16676,-427.73,0.0074834,0.18407,0.98289,-147.58

> view matrix models
> #5,0.90317,-0.42922,-0.0066065,-22.52,0.39554,0.83808,-0.37573,-362.74,0.16681,0.33674,0.9267,-200.51

> view matrix models
> #5,0.89285,-0.44665,0.057694,-30.421,0.44774,0.86654,-0.22051,-412.52,0.048498,0.22272,0.97368,-162.18

> view matrix models
> #5,0.95827,0.21943,0.18319,-208.53,-0.1872,0.96607,-0.17793,-309.49,-0.21602,0.13621,0.96684,-87.57

> ui mousemode right ""move picked models""

> view matrix models
> #5,0.95827,0.21943,0.18319,-65.576,-0.1872,0.96607,-0.17793,56.394,-0.21602,0.13621,0.96684,-13.032

> view matrix models
> #5,0.95827,0.21943,0.18319,-411.42,-0.1872,0.96607,-0.17793,53.196,-0.21602,0.13621,0.96684,84.331

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,0.95171,0.22036,0.21376,-416.74,-0.24459,0.96505,0.094094,7.5927,-0.18556,-0.14183,0.97234,134.31

> view matrix models
> #5,0.86834,-0.46825,-0.16348,-176.73,0.26519,0.7169,-0.64477,109.41,0.41911,0.51653,0.74669,-80.251

> view matrix models
> #5,0.89131,0.35369,-0.28368,-325.99,-0.39524,0.91269,-0.10389,91.972,0.22216,0.20472,0.95328,-18.51

> view matrix models
> #5,-0.23191,-0.73124,-0.64149,209.13,0.93481,0.014811,-0.35483,53.103,0.26897,-0.68196,0.68013,213.14

> view matrix models
> #5,-0.91802,0.35733,-0.17188,27.546,-0.16434,-0.73736,-0.6552,502.16,-0.36086,-0.57325,0.73564,310.46

> view matrix models
> #5,-0.77973,0.58391,-0.22598,-36.716,-0.46873,-0.78367,-0.40762,522.73,-0.41511,-0.21191,0.88475,215.38

> view matrix models
> #5,0.73487,0.66946,-0.10857,-395.82,-0.45634,0.36965,-0.80939,366.97,-0.50173,0.64434,0.57715,121.74

> view matrix models
> #5,0.8822,0.33885,0.32696,-450.77,-0.30763,0.94045,-0.14462,76.579,-0.35649,0.027,0.93391,143.27

> view matrix models
> #5,0.94884,0.21626,0.23005,-418.75,-0.16928,0.96347,-0.20754,56.282,-0.26653,0.15798,0.95079,93.793

> select up

201660 atoms, 214206 bonds, 18543 residues, 25 models selected  

> select subtract #12

201660 atoms, 214206 bonds, 18543 residues, 23 models selected  

> select subtract #10

201660 atoms, 214206 bonds, 18543 residues, 21 models selected  

> select subtract #9

201660 atoms, 214206 bonds, 18543 residues, 19 models selected  

> select subtract #11

201660 atoms, 214206 bonds, 18543 residues, 17 models selected  

> select add #13

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 20 models
selected  

> select subtract #13

16 models selected  

> select add #13

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 20 models
selected  

> select subtract #8

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 18 models
selected  

> select subtract #7

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 16 models
selected  

> select subtract #6

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 14 models
selected  

> select subtract #5

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 12 models
selected  

> select subtract #4

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 10 models
selected  

> select subtract #3

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 8 models
selected  

> select subtract #2

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 6 models
selected  

> select subtract #1

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 4 models
selected  

> select add #5

201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 6 models
selected  

> select subtract #13

2 models selected  

> volume flip #5

Opened cryosparc_P1_J98_001_volume_map_sharp.mrc z flip as #14, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> volume flip #6

Opened cryosparc_P1_J98_001_volume_map.mrc z flip as #15, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> select subtract #5

Nothing selected  

> select add #14

2 models selected  

> select subtract #14

Nothing selected  

> hide #!15 models

> select add #14

2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #14,0.94884,0.21626,0.23005,-200.24,-0.16928,0.96347,-0.20754,389.5,-0.26653,0.15798,0.95079,214.06

> view matrix models
> #14,0.94884,0.21626,0.23005,33.871,-0.16928,0.96347,-0.20754,311.45,-0.26653,0.15798,0.95079,80.444

> view matrix models
> #14,0.94884,0.21626,0.23005,44.353,-0.16928,0.96347,-0.20754,329.8,-0.26653,0.15798,0.95079,89.212

> ui mousemode right ""rotate selected models""

> view matrix models
> #14,-0.71291,0.41457,-0.56559,517.35,0.053037,0.8361,0.546,151.71,0.69925,0.35925,-0.61805,174.7

> view matrix models
> #14,-0.58449,0.65424,-0.47994,422.99,0.51395,0.75622,0.40495,101.5,0.62787,-0.0099738,-0.77825,299.56

> view matrix models
> #14,-0.8665,0.48146,-0.13182,444.67,0.43712,0.85936,0.26538,125.48,0.24105,0.17233,-0.95509,379.75

> ui mousemode right ""translate selected models""

> view matrix models
> #14,-0.8665,0.48146,-0.13182,311.43,0.43712,0.85936,0.26538,-133.04,0.24105,0.17233,-0.95509,298.98

> view matrix models
> #14,-0.8665,0.48146,-0.13182,301.97,0.43712,0.85936,0.26538,-136.62,0.24105,0.17233,-0.95509,310.84

> fitmap #14 inMap #1

Fit map cryosparc_P1_J98_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20953 points  
correlation = 0.9505, correlation about mean = 0.4196, overlap = 3.735e+04  
steps = 120, shift = 5.47, angle = 21.3 degrees  
  
Position of cryosparc_P1_J98_001_volume_map_sharp.mrc z flip (#14) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98107258 -0.17597274 -0.08080949 475.02696300  
0.18036378 -0.98229514 -0.05064740 396.29523914  
-0.07046621 -0.06426388 0.99544194 29.15789413  
Axis -0.03816849 -0.02899337 0.99885061  
Axis point 220.23575583 219.94877769 0.00000000  
Rotation angle (degrees) 169.72497776  
Shift along axis -0.49661611  
  

> select subtract #14

Nothing selected  

> hide #!14 models

> show #!15 models

> select add #15

2 models selected  

> view matrix models #15,1,0,0,-30.286,0,1,0,3.6156,0,0,1,-7.5317

> view matrix models #15,1,0,0,54.499,0,1,0,286.05,0,0,1,78.7

> ui mousemode right ""rotate selected models""

> view matrix models
> #15,0.38321,0.55433,-0.73883,223.3,-0.04452,0.81004,0.58468,211.72,0.92259,-0.19116,0.3351,66.212

> view matrix models
> #15,-0.60794,0.79331,0.032641,217.8,0.79308,0.60477,0.072661,187.69,0.037902,0.070061,-0.99682,475.37

> view matrix models
> #15,-0.76941,-0.038666,0.63758,295.68,-0.043359,0.99903,0.0082611,293.51,-0.63728,-0.021289,-0.77034,586.7

> view matrix models
> #15,-0.82432,0.035511,0.565,307.03,0.28199,0.89116,0.3554,175.4,-0.49089,0.45229,-0.74462,453.42

> view matrix models
> #15,-0.73021,0.40214,0.55234,214.67,0.61034,0.74726,0.26284,156.35,-0.30705,0.52905,-0.7911,409.24

> view matrix models
> #15,-0.99085,0.12541,0.049984,431.11,0.13499,0.92425,0.35714,198.71,-0.0014104,0.36062,-0.93271,410.24

> view matrix models
> #15,-0.79071,0.40291,0.46091,246.24,0.50008,0.85939,0.10664,188.9,-0.35314,0.31482,-0.88101,481.78

> ui mousemode right ""translate selected models""

> view matrix models
> #15,-0.79071,0.40291,0.46091,159.61,0.50008,0.85939,0.10664,-103.2,-0.35314,0.31482,-0.88101,387.36

> fitmap #15 inMap #1

Fit map cryosparc_P1_J98_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20969 points  
correlation = 0.9542, correlation about mean = 0.4157, overlap = 2.885e+04  
steps = 136, shift = 17.4, angle = 23.8 degrees  
  
Position of cryosparc_P1_J98_001_volume_map.mrc z flip (#15) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98115236 -0.17557997 -0.08069518 474.87459910  
0.17995399 -0.98237696 -0.05051806 396.33801347  
-0.07040312 -0.06408733 0.99545779 29.12375621  
Axis -0.03812219 -0.02891500 0.99885465  
Axis point 220.19725747 219.91262044 0.00000000  
Rotation angle (degrees) 169.74841221  
Shift along axis -0.47297300  
  

> hide #!5-6 target m

> hide #!15 models

> show #!7 models

> select add #7

4 models selected  

> view matrix models
> #7,1,0,0,139.29,0,1,0,237.58,0,0,1,70.239,#15,-0.7502,0.63514,0.18384,309.98,0.66091,0.712,0.23716,89.6,0.01973,0.29942,-0.95392,401.76

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.93246,0.33104,-0.1447,117.53,-0.3533,0.91924,-0.17369,364.71,0.075513,0.21308,0.97411,17.029,#15,-0.4836,0.78461,0.38796,179.73,0.86916,0.37811,0.31874,110.8,0.1034,0.49134,-0.86481,321.33

> view matrix models
> #7,0.90255,0.41887,-0.099714,96.482,-0.43047,0.88295,-0.18734,391.06,0.0095722,0.21201,0.97722,30.361,#15,-0.40222,0.84163,0.36039,155.49,0.9028,0.29916,0.30896,124.82,0.15222,0.44963,-0.88015,324.59

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.90255,0.41887,-0.099714,-59.667,-0.43047,0.88295,-0.18734,129.28,0.0095722,0.21201,0.97722,-64.029,#15,-0.40222,0.84163,0.36039,-0.6584,0.9028,0.29916,0.30896,-136.96,0.15222,0.44963,-0.88015,230.2

> view matrix models
> #7,0.90255,0.41887,-0.099714,32.414,-0.43047,0.88295,-0.18734,453.43,0.0095722,0.21201,0.97722,139.71,#15,-0.40222,0.84163,0.36039,91.423,0.9028,0.29916,0.30896,187.19,0.15222,0.44963,-0.88015,433.95

> view matrix models
> #7,0.90255,0.41887,-0.099714,28.655,-0.43047,0.88295,-0.18734,445.31,0.0095722,0.21201,0.97722,119.74,#15,-0.40222,0.84163,0.36039,87.664,0.9028,0.29916,0.30896,179.08,0.15222,0.44963,-0.88015,413.97

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.99429,-0.062625,0.086398,66.861,0.081239,0.96923,-0.23237,330.61,-0.069187,0.23807,0.96878,132.74,#15,-0.7856,0.61279,0.085524,274.48,0.57505,0.67211,0.46646,124.01,0.22836,0.41563,-0.8804,406.87

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.99429,-0.062625,0.086398,-17.957,0.081239,0.96923,-0.23237,29.936,-0.069187,0.23807,0.96878,-50.171,#15,-0.7856,0.61279,0.085524,189.66,0.57505,0.67211,0.46646,-176.66,0.22836,0.41563,-0.8804,223.97

> fitmap #7 inMap #1

Fit map cryosparc_P1_J103_001_volume_map_sharp.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20957 points  
correlation = 0.6005, correlation about mean = 0.05396, overlap = 1.802e+04  
steps = 148, shift = 14.4, angle = 17.8 degrees  
  
Position of cryosparc_P1_J103_001_volume_map_sharp.mrc (#7) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.76581617 -0.61952749 0.17236961 147.91850026  
-0.62449626 -0.78043353 -0.03046179 517.53025941  
0.15339494 -0.08431604 -0.98456122 406.01213584  
Axis -0.93961909 0.33105949 -0.08669243  
Axis point 0.00000000 287.91796449 192.22828107  
Rotation angle (degrees) 178.35782179  
Shift along axis -2.85192000  
  

> hide #!7 models

> select subtract #7

2 models selected  

> volume flip #7

Opened cryosparc_P1_J103_001_volume_map_sharp.mrc z flip as #16, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> volume flip #8

Opened cryosparc_P1_J103_001_volume_map.mrc z flip as #17, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> select subtract #15

Nothing selected  

> select add #16

2 models selected  

> select add #17

4 models selected  

> view matrix models
> #16,0.97661,0.20537,-0.06361,295.5,-0.2149,0.94132,-0.26027,79.798,0.0064257,0.26785,0.96344,-42.97,#17,1,0,0,343.73,0,1,0,-13.806,0,0,1,22.177

> select subtract #16

2 models selected  

> select subtract #17

Nothing selected  

> hide #!17 models

> select add #16

2 models selected  

> view matrix models
> #16,0.97661,0.20537,-0.06361,494.67,-0.2149,0.94132,-0.26027,42.666,0.0064257,0.26785,0.96344,-125.77

> view matrix models
> #16,0.97661,0.20537,-0.06361,539.22,-0.2149,0.94132,-0.26027,-157.44,0.0064257,0.26785,0.96344,-126.98

> view matrix models
> #16,0.97661,0.20537,-0.06361,136.85,-0.2149,0.94132,-0.26027,-224.63,0.0064257,0.26785,0.96344,-222.21

> view matrix models
> #16,0.97661,0.20537,-0.06361,-269,-0.2149,0.94132,-0.26027,-278.64,0.0064257,0.26785,0.96344,-341.12

> view matrix models
> #16,0.97661,0.20537,-0.06361,26.1,-0.2149,0.94132,-0.26027,-225.38,0.0064257,0.26785,0.96344,-277.91

> view matrix models
> #16,0.97661,0.20537,-0.06361,-159.13,-0.2149,0.94132,-0.26027,-168.48,0.0064257,0.26785,0.96344,-246.2

> ui mousemode right ""rotate selected models""

> view matrix models
> #16,-0.98171,0.0053892,0.19029,237.31,0.096549,0.87559,0.47331,-373.57,-0.16406,0.48302,-0.8601,127.03

> view matrix models
> #16,-0.84457,0.49586,0.20204,107.34,0.53544,0.77975,0.3245,-414.86,0.0033646,0.38224,-0.92406,125.72

> ui mousemode right ""translate selected models""

> view matrix models
> #16,-0.84457,0.49586,0.20204,299.51,0.53544,0.77975,0.3245,-395.68,0.0033646,0.38224,-0.92406,143.4

> view matrix models
> #16,-0.84457,0.49586,0.20204,214.76,0.53544,0.77975,0.3245,-156.89,0.0033646,0.38224,-0.92406,305.37

> fitmap #16 inMap #1

Fit map cryosparc_P1_J103_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20957 points  
correlation = 0.9755, correlation about mean = 0.5526, overlap = 5.308e+04  
steps = 92, shift = 5.53, angle = 9.25 degrees  
  
Position of cryosparc_P1_J103_001_volume_map_sharp.mrc z flip (#16) relative
to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96683848 -0.25490298 -0.01574208 475.52480895  
0.25537198 -0.96564058 -0.04820192 375.16923347  
-0.00291438 -0.05062355 0.99871355 13.27964100  
Axis -0.00474420 -0.02513058 0.99967292  
Axis point 213.44254341 218.61395610 0.00000000  
Rotation angle (degrees) 165.21332178  
Shift along axis 1.59109330  
  

> hide #!16 models

> select subtract #16

Nothing selected  

> show #!17 models

> select add #17

2 models selected  

> view matrix models #17,1,0,0,458.15,0,1,0,-248.2,0,0,1,128.02

> view matrix models #17,1,0,0,330.11,0,1,0,-505.1,0,0,1,-181.44

> view matrix models #17,1,0,0,-110.63,0,1,0,-103.45,0,0,1,-51.961

> view matrix models #17,1,0,0,-220.22,0,1,0,-330.26,0,0,1,-96.103

> ui mousemode right ""rotate selected models""

> view matrix models
> #17,-0.99562,0.075776,-0.05482,191.89,0.046339,0.90881,0.41463,-408.19,0.08124,0.41027,-0.90834,203.05

> view matrix models
> #17,-0.72947,0.68402,-0.00018359,2.5397,0.66833,0.71279,0.21277,-456.18,0.14567,0.15508,-0.9771,255.37

> ui mousemode right ""translate selected models""

> view matrix models
> #17,-0.72947,0.68402,-0.00018359,283.49,0.66833,0.71279,0.21277,-354.27,0.14567,0.15508,-0.9771,306.93

> view matrix models
> #17,-0.72947,0.68402,-0.00018359,147.46,0.66833,0.71279,0.21277,-183.03,0.14567,0.15508,-0.9771,346.62

> fitmap #17 inMap #1

Fit map cryosparc_P1_J103_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20954 points  
correlation = 0.9824, correlation about mean = 0.608, overlap = 3.677e+04  
steps = 152, shift = 63.8, angle = 14.7 degrees  
  
Position of cryosparc_P1_J103_001_volume_map.mrc z flip (#17) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96677903 -0.25511364 -0.01597928 475.61770509  
0.25559328 -0.96559949 -0.04785078 375.06880806  
-0.00322220 -0.05034533 0.99872667 13.27362394  
Axis -0.00488292 -0.02497117 0.99967625  
Axis point 213.47529806 218.59546722 0.00000000  
Rotation angle (degrees) 165.20056891  
Shift along axis 1.58101585  
  

> hide #!17 models

> select subtract #17

Nothing selected  

> show #!9 models

> select add #9

2 models selected  

> view matrix models #9,1,0,0,66.813,0,1,0,132.93,0,0,1,25.089

> view matrix models #9,1,0,0,-5.4711,0,1,0,-10.379,0,0,1,-14.373

> view matrix models #9,1,0,0,213.16,0,1,0,-70.987,0,0,1,35.886

> hide #!9 models

> select subtract #9

Nothing selected  

> volume flip #9

Opened cryosparc_P1_J104_001_volume_map_sharp.mrc z flip as #18, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> volume flip #10

Opened cryosparc_P1_J104_001_volume_map.mrc z flip as #19, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> hide #!18 models

> hide #!19 models

> show #!11 models

> show #!12 models

> hide #!11 models

> select add #12

2 models selected  

> view matrix models #12,1,0,0,268.63,0,1,0,-66.479,0,0,1,23.067

> volume #12 level 0.5398

> view matrix models #12,1,0,0,81.495,0,1,0,87.616,0,0,1,-20.101

> view matrix models #12,1,0,0,194.71,0,1,0,264.02,0,0,1,105.21

> ui mousemode right ""rotate selected models""

> view matrix models
> #12,-0.10029,-0.84368,-0.5274,717.92,0.76343,0.27468,-0.58458,398.49,0.63806,-0.46126,0.61654,162.58

> view matrix models
> #12,0.81932,0.56752,0.081469,83.468,0.53406,-0.70377,-0.46849,645.77,-0.20854,0.42735,-0.8797,435.7

> ui mousemode right ""translate selected models""

> view matrix models
> #12,0.81932,0.56752,0.081469,-105.79,0.53406,-0.70377,-0.46849,334.74,-0.20854,0.42735,-0.8797,319.82

> fitmap #12 inMap #1

Fit map cryosparc_P1_J108_001_volume_map.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 50668 points  
correlation = 0.581, correlation about mean = 0.06365, overlap = 1.908e+04  
steps = 88, shift = 12.6, angle = 9.87 degrees  
  
Position of cryosparc_P1_J108_001_volume_map.mrc (#12) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.06114525 0.83113550 0.55269794 -90.61961165  
-0.92970330 -0.15406746 0.33453694 367.12907629  
0.36319830 -0.53430045 0.76328894 98.33563139  
Axis -0.44044208 0.09606357 -0.89262678  
Axis point 105.13661117 234.46921583 0.00000000  
Rotation angle (degrees) 99.48658293  
Shift along axis -12.59659896  
  

> hide #!12 models

> show #!12 models

> select subtract #12

Nothing selected  

> hide #!12 models

> volume flip #11

Opened cryosparc_P1_J108_001_volume_map_sharp.mrc z flip as #20, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> volume flip #12

Opened cryosparc_P1_J108_001_volume_map.mrc z flip as #21, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> hide #!20 models

> hide #!21 models

> color #21 #ff8ad8ff models

> color #20 #8efa00ff models

> show #!20 models

> show #!21 models

> select add #20

2 models selected  

> select add #21

4 models selected  

> view matrix models
> #20,1,0,0,53.202,0,1,0,-7.5989,0,0,1,190.93,#21,0.82238,0.52086,0.22892,-84.958,0.55466,-0.64438,-0.52644,319.91,-0.12669,0.5599,-0.81882,459.54

> view matrix models
> #20,1,0,0,67.39,0,1,0,-20.44,0,0,1,252.74,#21,0.82238,0.52086,0.22892,-70.77,0.55466,-0.64438,-0.52644,307.07,-0.12669,0.5599,-0.81882,521.35

> hide #!21 models

> select subtract #21

2 models selected  

> select subtract #20

Nothing selected  

> color #20 #009051ff models

> ui mousemode right ""rotate selected models""

> select add #20

2 models selected  

> view matrix models
> #20,0.27636,0.8512,-0.44618,112.44,-0.80283,0.45968,0.37969,170.16,0.52829,0.25328,0.8104,137.01

> view matrix models
> #20,-0.65371,-0.13935,0.7438,253.23,0.71992,-0.41741,0.55452,37.04,0.2332,0.89797,0.37319,144.31

> view matrix models
> #20,0.46888,-0.87548,0.11701,336.56,0.75284,0.46541,0.46543,-145.06,-0.46193,-0.13015,0.87731,395.51

> view matrix models
> #20,-0.21802,-0.91836,0.33028,430.92,0.9553,-0.27006,-0.12031,104.18,0.19968,0.28929,0.93618,164.59

> ui mousemode right ""translate selected models""

> view matrix models
> #20,-0.21802,-0.91836,0.33028,360.58,0.9553,-0.27006,-0.12031,68.863,0.19968,0.28929,0.93618,-101.25

> fitmap #20 inMap #1

Fit map cryosparc_P1_J108_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20960 points  
correlation = 0.9607, correlation about mean = 0.5065, overlap = 3.58e+04  
steps = 164, shift = 19, angle = 31.6 degrees  
  
Position of cryosparc_P1_J108_001_volume_map_sharp.mrc z flip (#20) relative
to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.69739435 -0.66663667 0.26312861 446.13461962  
-0.64054491 0.41508898 -0.64606760 393.09938307  
0.32147057 -0.61910959 -0.71649144 437.78580544  
Axis 0.38864826 -0.84110432 0.37615961  
Axis point 309.40142148 0.00000000 311.36461851  
Rotation angle (degrees) 178.01248299  
Shift along axis 7.42918773  
  

> hide #!20 models

> select subtract #20

Nothing selected  

> show #!21 models

> select add #21

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #21,-0.21616,-0.86898,0.44513,410.44,0.96297,-0.26498,-0.049669,34.863,0.16111,0.41792,0.89409,126.05

> view matrix models
> #21,-0.11346,-0.8849,0.45175,392.11,0.98636,-0.15491,-0.05571,6.1447,0.11928,0.43927,0.8904,130.3

> ui mousemode right ""translate selected models""

> view matrix models
> #21,-0.11346,-0.8849,0.45175,337,0.98636,-0.15491,-0.05571,11.919,0.11928,0.43927,0.8904,-124.26

> fitmap #21 inMap #1

Fit map cryosparc_P1_J108_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 50668 points  
correlation = 0.9363, correlation about mean = 0.5935, overlap = 4.442e+04  
steps = 152, shift = 35.3, angle = 21.8 degrees  
  
Position of cryosparc_P1_J108_001_volume_map.mrc z flip (#21) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.69726654 -0.66670565 0.26329245 446.12009666  
-0.64067666 0.41490792 -0.64605324 393.19130505  
0.32148523 -0.61915665 -0.71644417 437.79327448  
Axis 0.38873206 -0.84105079 0.37619271  
Axis point 309.45157406 0.00000000 311.39100265  
Rotation angle (degrees) 178.01744087  
Shift along axis 7.42196968  
  

> hide #!21 models

> select subtract #21

Nothing selected  

> show #!19 models

> select add #19

2 models selected  

> view matrix models #19,1,0,0,-42.02,0,1,0,18.881,0,0,1,314.82

> ui mousemode right ""rotate selected models""

> view matrix models
> #19,0.92212,-0.028777,0.38583,-100.57,-0.24883,0.71952,0.64836,-7.1838,-0.29627,-0.69388,0.65632,591.17

> view matrix models
> #19,0.99752,0.017141,0.068256,-59.305,-0.025979,0.99107,0.13078,-1.2232,-0.065404,-0.13223,0.98906,357.94

> view matrix models
> #19,0.9668,-0.13527,-0.21679,38.066,0.016927,0.88043,-0.47387,139.06,0.25497,0.45447,0.85349,198.86

> view matrix models
> #19,-0.49114,0.42795,0.75871,27.093,0.85871,0.38412,0.33922,-108.28,-0.14627,0.81812,-0.55614,505.13

> view matrix models
> #19,-0.47256,-0.0534,0.87968,96.019,0.65138,0.65118,0.38945,-129.43,-0.59362,0.75704,-0.27294,552.87

> view matrix models
> #19,-0.57038,0.12072,0.81246,95.281,0.42332,0.89086,0.16482,-82.984,-0.70389,0.43794,-0.55923,701.35

> view matrix models
> #19,-0.65223,0.20302,0.73033,113.03,0.25959,0.96503,-0.036441,-21.272,-0.71219,0.16582,-0.68212,784.4

> view matrix models
> #19,-0.58584,0.1396,0.79831,97.665,0.39097,0.91153,0.12751,-72.533,-0.70988,0.38682,-0.58859,719.2

> view matrix models
> #19,-0.50292,0.01387,0.86422,91.957,0.57494,0.75195,0.32251,-119.79,-0.64538,0.65908,-0.38615,607.55

> view matrix models
> #19,-0.46848,-0.063909,0.88116,96.988,0.66228,0.63471,0.39815,-130.2,-0.58473,0.7701,-0.25503,544.57

> view matrix models
> #19,-0.57142,0.43933,0.69316,55.504,0.79737,0.497,0.34233,-118.99,-0.1941,0.74832,-0.63431,545.88

> view matrix models
> #19,-0.61617,0.64013,0.45888,73.124,0.74524,0.66237,0.0767,-86,-0.25485,0.38923,-0.88518,684.62

> ui mousemode right ""translate selected models""

> view matrix models
> #19,-0.61617,0.64013,0.45888,101.76,0.74524,0.66237,0.0767,-131.88,-0.25485,0.38923,-0.88518,367.72

> fitmap #19 inMap #1

Fit map cryosparc_P1_J104_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20967 points  
correlation = 0.9772, correlation about mean = 0.6042, overlap = 3.685e+04  
steps = 116, shift = 25.4, angle = 15.8 degrees  
  
Position of cryosparc_P1_J104_001_volume_map.mrc z flip (#19) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98947893 -0.14464668 0.00295998 453.74695953  
0.14458261 -0.98936543 -0.01587127 396.30669175  
0.00522423 -0.01527633 0.99986965 2.25096215  
Axis 0.00205693 -0.00782830 0.99996724  
Axis point 212.46654917 214.65452905 0.00000000  
Rotation angle (degrees) 171.68476065  
Shift along axis 0.08180356  
  

> select subtract #19

Nothing selected  

> hide #!19 models

> show #!18 models

> select add #18

2 models selected  

> view matrix models #18,1,0,0,17.023,0,1,0,-45.334,0,0,1,132.41

> view matrix models #18,1,0,0,61.372,0,1,0,-65.864,0,0,1,274.99

> ui mousemode right ""move picked models""

> view matrix models #18,1,0,0,70.962,0,1,0,-60.184,0,0,1,300.78

> ui mousemode right ""move picked models""

> view matrix models #18,1,0,0,68.685,0,1,0,-62.07,0,0,1,294.92

> ui mousemode right ""rotate selected models""

> view matrix models
> #18,-0.74784,0.64006,-0.17624,344.71,0.61749,0.76812,0.16939,-181.02,0.24379,0.017855,-0.96966,655.34

> view matrix models
> #18,-0.21411,0.5917,0.77721,40.569,0.73477,0.62183,-0.27099,-83.023,-0.64364,0.51305,-0.5679,657.09

> view matrix models
> #18,-0.72069,0.48857,0.49183,228.93,0.63686,0.74687,0.19129,-185.39,-0.27387,0.45109,-0.84942,650.97

> ui mousemode right ""translate selected models""

> view matrix models
> #18,-0.72069,0.48857,0.49183,291.93,0.63686,0.74687,0.19129,-210.76,-0.27387,0.45109,-0.84942,358.77

> view matrix models
> #18,-0.72069,0.48857,0.49183,179.04,0.63686,0.74687,0.19129,-177.75,-0.27387,0.45109,-0.84942,251.83

> view matrix models
> #18,-0.72069,0.48857,0.49183,128.54,0.63686,0.74687,0.19129,-142.08,-0.27387,0.45109,-0.84942,334.07

> fitmap #18 inMap #1

Fit map cryosparc_P1_J104_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20955 points  
correlation = 0.9714, correlation about mean = 0.5654, overlap = 5.321e+04  
steps = 128, shift = 4.2, angle = 19.3 degrees  
  
Position of cryosparc_P1_J104_001_volume_map_sharp.mrc z flip (#18) relative
to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98953295 -0.14427756 0.00292143 453.69602792  
0.14421537 -0.98942289 -0.01562912 396.34010493  
0.00514547 -0.01504421 0.99987359 2.19822617  
Axis 0.00202739 -0.00770889 0.99996823  
Axis point 212.47705459 214.62658713 0.00000000  
Rotation angle (degrees) 171.70608844  
Shift along axis 0.06263310  
  

> select subtract #18

Nothing selected  

> hide #!18 models

> show #!17 models

> hide #!17 models

> volume #1 level 0.7168

> surface dust #1 size 33.2

> hide #!1 models

> show #!14 models

> show #!15 models

> hide #!14 models

> hide #!15 models

> show #!15 models

> show #!14 models

> fitmap #15 inMap #14

Fit map cryosparc_P1_J98_001_volume_map.mrc z flip in map
cryosparc_P1_J98_001_volume_map_sharp.mrc z flip using 20969 points  
correlation = 0.9933, correlation about mean = 0.872, overlap = 3.502e+04  
steps = 124, shift = 27.2, angle = 14.9 degrees  
  
Position of cryosparc_P1_J98_001_volume_map.mrc z flip (#15) relative to
cryosparc_P1_J98_001_volume_map_sharp.mrc z flip (#14) coordinates:  
Matrix rotation and translation  
1.00000001 -0.00004692 -0.00002196 -0.00759824  
0.00004692 0.99999999 0.00012920 -0.05710014  
0.00002196 -0.00012920 1.00000000 0.00947988  
Axis -0.92817399 -0.15775244 0.33705670  
Axis point 0.00000000 23.11236043 418.44568493  
Rotation angle (degrees) 0.00797543  
Shift along axis 0.01925543  
  

> volume #14 level 0.5902

> volume #15 level 0.2948

> surface dust #14 size 33.2

> surface dust #15 size 33.2

> hide #!14 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!2 models

> show #!1 models

> hide #!2 models

> volume #1 level 0.3519

> ui mousemode right ""mark point""

> marker #22 position 156.8,222.4,140.8 color #d783ff radius 5

> marker #22 position 154.5,221.6,141 color #d783ff radius 5

> hide #!1 models

> ui mousemode right ""delete markers""

> hide #22 target m

> show #!1 models

> select add #22

3 atoms, 3 residues, 1 model selected  

> select subtract #22

Nothing selected  

> show #22 models

> hide #!1 models

> hide #22 target m

> close #22

> show #!1 models

> ui mousemode right ""mark plane""

> ui mousemode right ""mark point""

> marker #22 position 174.3,163.2,167.1 color #d783ff radius 5

> ui mousemode right ""move markers""

> hide #!1 models

> marker change #22:1 position 154.8,168.4,139.2

> ui mousemode right ""delete markers""

> marker delete #22:2

> ui mousemode right ""move markers""

> close #22

> show #!1 models

> ui mousemode right ""move markers""

> ui mousemode right ""mark point""

> marker #22 position 176.4,193.4,182.5 color #d783ff radius 5

> marker #22 position 176.4,193.4,182.6 color #d783ff radius 5

> hide #!1 models

> ui mousemode right ""delete markers""

> marker delete #22:2

> marker delete #22:1

> show #!1 models

> ui mousemode right ""mark point""

> marker #22 position 166,182.7,180.8 color #d783ff radius 5

> marker #22 position 166,182.8,181.9 color #d783ff radius 5

> marker #22 position 171.9,186.3,185.4 color #d783ff radius 5

> marker #22 position 172.2,186.4,185.5 color #d783ff radius 5

> hide #!1 models

> ui mousemode right ""delete markers""

> marker delete #22:4

> marker delete #22:3

> ui mousemode right ""move markers""

> select add #22

2 atoms, 2 residues, 1 model selected  

> marker change #22:1 position 153.9,198.1,208.6

> ui mousemode right ""delete markers""

> ~select

Nothing selected  

> ui mousemode right ""move markers""

> ui mousemode right ""resize markers""

> marker change #22:2 radius 5

> ui mousemode right ""delete markers""

> marker delete #22:1

> ui mousemode right ""move markers""

> ui mousemode right ""resize markers""

> marker change #22:2 radius 21.07

> ui mousemode right ""move markers""

> marker change #22:2 position 135.7,190,200.8

> show #!1 models

> marker change #22:2 position 197.4,124.4,201.9

> marker change #22:2 position 193.5,130.4,178.4

> marker change #22:2 position 189.4,129.1,178.4

> hide #!1 models

> show #!1 models

> hide #22 models

> show #22 models

> select add #22

1 atom, 1 residue, 1 model selected  

> transparency #22 20

> transparency #22 80

> transparency sel 80

> marker change #22 color #d49df9

> marker change #22 color #d39cf7

> marker change #22 color #cd97f1

> marker change #22 color #c18fe3

> marker change #22 color #ac7fca

> marker change #22 color #a57ac2

> marker change #22 color #a177bd

> marker change #22 color #9e74b9

> marker change #22 color #9d74b8

> marker change #22 color #9b73b6

> marker change #22 color #9871b3

> marker change #22 color #956eaf

> marker change #22 color #936dad

> marker change #22 color #926cab

> marker change #22 color #916baa

> marker change #22 color #8f6aa8

> marker change #22 color #8e69a7

> marker change #22 color #8d68a6

> marker change #22 color #8c68a5

> marker change #22 color #8a66a2

> marker change #22 color #8965a0

> marker change #22 color #86639d

> marker change #22 color #805e96

> marker change #22 color #7e5d93

> marker change #22 color #7d5c93

> marker change #22 color #7c5b91

> marker change #22 color #7a5a90

> marker change #22 color #78598d

> marker change #22 color #76578a

> marker change #22 color #735588

> marker change #22 color #715485

> marker change #22 color #6e5181

> marker change #22 color #6c507f

> marker change #22 color #6b4f7d

> marker change #22 color #684d7a

> marker change #22 color #664c78

> marker change #22 color #654b77

> marker change #22 color #634974

> marker change #22 color #624873

> marker change #22 color #614872

> marker change #22 color #604771

> marker change #22 color #5f4670

> marker change #22 color #5e466f

> marker change #22 color #5d456e

> marker change #22 color #5c446c

> marker change #22 color #5a436a

> marker change #22 color #594168

> marker change #22 color #584167

> marker change #22 color #553f64

> marker change #22 color #523d60

> marker change #22 color #503b5e

> marker change #22 color #4f3a5d

> marker change #22 color #4c385a

> marker change #22 color #4a3656

> marker change #22 color #473554

> marker change #22 color #453351

> marker change #22 color #402f4b

> marker change #22 color #3d2d47

> marker change #22 color #392a43

> marker change #22 color #372941

> marker change #22 color #34273d

> marker change #22 color #31243a

> marker change #22 color #2e2236

> marker change #22 color #2b2033

> marker change #22 color #271d2e

> marker change #22 color #251b2c

> marker change #22 color #241b2a

> marker change #22 color #241a2a

> marker change #22 color #231a29

> marker change #22 color #221928

> marker change #22 color #231a29

> marker change #22 color #241b2b

> marker change #22 color #302439

> marker change #22 color #402f4b

> marker change #22 color #503b5e

> marker change #22 color #624873

> marker change #22 color #a77bc4

> marker change #22 color #b989da

> marker change #22 color #c592e7

> marker change #22 color #cd97f0

> marker change #22 color #cf99f3

> marker change #22 color #d29bf7

> marker change #22 color #d49cf8

> marker change #22 color #d49cf9

> marker change #22 color #d69efb

> marker change #22:2 position 182.9,125.9,177.7

> marker change #22:2 position 187.8,127.5,181.3

> marker change #22:2 position 189.3,128.5,182.8

> transparency #22 80

> transparency 80

> transparency 0

> transparency sel 60

> color #22 #d69efb80

> marker change #22:2 position 191.1,132.5,186.9

> color zone #1 near #22 distance 3

> hide #22 models

> show #22 models

> ui mousemode right ""translate selected models""

> view matrix models #22,1,0,0,-1.1495,0,1,0,6.218,0,0,1,-5.4765

> color zone #1 near #22 distance 10

> hide #22 models

> show #22 models

> view matrix models #22,1,0,0,-2.0282,0,1,0,9.2927,0,0,1,-7.23

> view matrix models #22,1,0,0,-2.0371,0,1,0,8.9451,0,0,1,-6.0522

> view matrix models #22,1,0,0,-4.2482,0,1,0,9.8188,0,0,1,-5.3853

> color zone #1 near #22 distance 10

> hide #22 models

> show #22 models

> measure center #22

Center of mass of 1 atoms = (186.81, 142.31, 181.50)  

> color zone #1 center 186.81, 142.31, 181.50 dis 20

Expected a keyword  

> color zone #1 near #22 distance 20

> hide #22 models

> show #22 models

> save ""/Users/haandrew/Documents/progress/2026/Cryo-EM/working session 2026
> .tif"" width 864 height 587 supersample 3

> save ""/Users/haandrew/Documents/progress/2026/Cryo-EM/working session
> 2026.cxs""

> hide #22 models

> select subtract #22

Nothing selected  

> close session

> open ""/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /100625_allmaps
> overlay .cxs""

Opened ec8 ribso _ cryosparc_P26_J24_001_volume_map.mrc as #1, grid size
128,128,128, pixel 3.35, shown at level 1.07, step 1, values float32  
Opened cryosparc_P1_J21_class_04_00082_volume.mrc as #2, grid size
128,128,128, pixel 3.32, shown at level 0.34, step 1, values float32  
Opened cryosparc_P1_J21_class_03_00082_volume.mrc as #3, grid size
128,128,128, pixel 3.32, shown at level 0.108, step 1, values float32  
Opened cryosparc_P1_J21_class_02_00082_volume.mrc as #4, grid size
128,128,128, pixel 3.32, shown at level 0.0537, step 1, values float32  
Opened cryosparc_P1_J21_class_01_00082_volume.mrc as #5, grid size
128,128,128, pixel 3.32, shown at level 0.303, step 1, values float32  
Opened cryosparc_P1_J21_class_00_00082_volume.mrc as #6, grid size
128,128,128, pixel 3.32, shown at level 0.249, step 1, values float32  
Opened cryosparc_P1_J21_class_00_00082_volume.mrc z flip as #7, grid size
128,128,128, pixel 3.32, shown at level 0.311, step 1, values float32  
Opened cryosparc_P1_J21_class_01_00082_volume.mrc z flip as #8, grid size
128,128,128, pixel 3.32, shown at level 0.498, step 1, values float32  
opened ChimeraX session  

> close session

> open ""/Users/haandrew/Documents/progress/2025/Cryo-
> EM/20250506_scRibso_SND1/maps/best session.cxs""

Opened cryosparc_P1_J22_class_00_00062_volume_sharp.mrc as #1.1, grid size
128,128,128, pixel 3.35, shown at level 0.391, step 1, values float32  
Opened cryosparc_P1_J22_class_04_00062_volume_sharp.mrc as #1.2, grid size
128,128,128, pixel 3.35, shown at level 0.715, step 1, values float32  
Opened cryosparc_P1_J22_class_03_00062_volume_sharp.mrc as #1.3, grid size
128,128,128, pixel 3.35, shown at level 0.425, step 1, values float32  
Opened cryosparc_P1_J22_class_02_00062_volume_sharp.mrc as #1.4, grid size
128,128,128, pixel 3.35, shown at level 0.731, step 1, values float32  
Opened cryosparc_P1_J22_class_01_00062_volume_sharp.mrc as #1.5, grid size
128,128,128, pixel 3.35, shown at level 0.169, step 1, values float32  
Opened apo ribso _ cryosparc_P26_J24_001_volume_map.mrc as #1.6, grid size
128,128,128, pixel 3.35, shown at level 1.13, step 1, values float32  
Opened cryosparc_P1_J22_class_00_00062_volume_sharp.mrc z flip as #2, grid
size 128,128,128, pixel 3.35, shown at level 0.471, step 1, values float32  
Opened cryosparc_P1_J22_class_03_00062_volume_sharp.mrc z flip as #3, grid
size 128,128,128, pixel 3.35, shown at level 0.443, step 1, values float32  
Opened cryosparc_P1_J22_class_03_00062_volume_sharp.mrc z flip z flip as #4,
grid size 128,128,128, pixel 3.35, shown at level 0.265, step 1, values
float32  
Opened cryosparc_P1_J22_class_02_00062_volume_sharp.mrc z flip as #6, grid
size 128,128,128, pixel 3.35, shown at level 0.564, step 1, values float32  
Opened cryosparc_P1_J22_class_01_00062_volume_sharp.mrc z flip z flip as #7,
grid size 128,128,128, pixel 3.35, shown at level 0.28, step 1, values float32  
Opened apo ribso _ cryosparc_P26_J24_001_volume_map.mrc as #8, grid size
128,128,128, pixel 3.35, shown at level 0.693, step 1, values float32  
Opened apo ribso _ cryosparc_P26_J24_001_volume_map.mrc z flip as #9, grid
size 128,128,128, pixel 3.35, shown at level 2.85, step 1, values float32  
Opened focmap trna.mrc as #13, grid size 128,128,128, pixel 3.35, shown at
level 0.063, step 1, values float32  
Opened cryosparc_P1_J22_class_00_00062_volume_sharp.mrc as #14, grid size
128,128,128, pixel 3.35, shown at level 1.35, step 1, values float32  

> set bgColor #ffffff00

opened ChimeraX session  
Showing cryosparc_P1_J22_class_00_00062_volume_sharp z flip.seg - 18 regions,
18 surfaces  

> volume #14 level 0.405

> ui tool show ""Side View""

> lighting full

> lighting shadows false

> lighting flat

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting soft

> set bgColor black

> set bgColor transparent

> hide #!5 models

> show #!5 models

> hide #!14 models

> hide #!13 models

> close session

> open ""/Users/haandrew/Documents/progress/2026/Cryo-EM/working session
> 2026.cxs"" format session

Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #1, grid size 128,128,128,
pixel 3.32, shown at level 0.352, step 1, values float32  
Opened cryosparc_P1_J49_001_volume_map.mrc as #2, grid size 128,128,128, pixel
3.32, shown at level 1.03, step 1, values float32  
Opened cryosparc_P1_J97_002_volume_map_sharp.mrc as #3, grid size 128,128,128,
pixel 3.32, shown at level 0.389, step 1, values float32  
Opened cryosparc_P1_J97_002_volume_map.mrc as #4, grid size 128,128,128, pixel
3.32, shown at level 0.721, step 1, values float32  
Opened cryosparc_P1_J98_001_volume_map_sharp.mrc as #5, grid size 128,128,128,
pixel 3.32, shown at level 1.11, step 1, values float32  
Opened cryosparc_P1_J98_001_volume_map.mrc as #6, grid size 128,128,128, pixel
3.32, shown at level 0.905, step 1, values float32  
Opened cryosparc_P1_J103_001_volume_map_sharp.mrc as #7, grid size
128,128,128, pixel 3.32, shown at level 1.41, step 1, values float32  
Opened cryosparc_P1_J103_001_volume_map.mrc as #8, grid size 128,128,128,
pixel 3.32, shown at level 1.04, step 1, values float32  
Opened cryosparc_P1_J104_001_volume_map_sharp.mrc as #9, grid size
128,128,128, pixel 3.32, shown at level 1.4, step 1, values float32  
Opened cryosparc_P1_J104_001_volume_map.mrc as #10, grid size 128,128,128,
pixel 3.32, shown at level 1.04, step 1, values float32  
Opened cryosparc_P1_J108_001_volume_map_sharp.mrc as #11, grid size
128,128,128, pixel 3.32, shown at level 1.01, step 1, values float32  
Opened cryosparc_P1_J108_001_volume_map.mrc as #12, grid size 128,128,128,
pixel 3.32, shown at level 0.54, step 1, values float32  
Opened cryosparc_P1_J98_001_volume_map_sharp.mrc z flip as #14, grid size
128,128,128, pixel 3.32, shown at level 0.59, step 1, values float32  
Opened cryosparc_P1_J98_001_volume_map.mrc z flip as #15, grid size
128,128,128, pixel 3.32, shown at level 0.295, step 1, values float32  
Opened cryosparc_P1_J103_001_volume_map_sharp.mrc z flip as #16, grid size
128,128,128, pixel 3.32, shown at level 1.41, step 1, values float32  
Opened cryosparc_P1_J103_001_volume_map.mrc z flip as #17, grid size
128,128,128, pixel 3.32, shown at level 1.04, step 1, values float32  
Opened cryosparc_P1_J104_001_volume_map_sharp.mrc z flip as #18, grid size
128,128,128, pixel 3.32, shown at level 1.4, step 1, values float32  
Opened cryosparc_P1_J104_001_volume_map.mrc z flip as #19, grid size
128,128,128, pixel 3.32, shown at level 1.04, step 1, values float32  
Opened cryosparc_P1_J108_001_volume_map_sharp.mrc z flip as #20, grid size
128,128,128, pixel 3.32, shown at level 1.01, step 1, values float32  
Opened cryosparc_P1_J108_001_volume_map.mrc z flip as #21, grid size
128,128,128, pixel 3.32, shown at level 0.54, step 1, values float32  
opened ChimeraX session  

> select zone #1 near #22 dis 20

Missing or invalid ""range"" argument: Expected a number  

> select zone #1 near #22 dis 20

Missing or invalid ""range"" argument: Expected a number  

> select zone #1 near #22 dis 10

Missing or invalid ""range"" argument: Expected a number  

> view matrix models #22,1,0,0,-2.2078,0,1,0,10.085,0,0,1,-6.0799

> select zone #1 in #22

Missing or invalid ""range"" argument: Expected a number  

> select zone #1 on #22

Missing or invalid ""range"" argument: Expected a number  

> view matrix models #22,1,0,0,-3.4988,0,1,0,9.7971,0,0,1,-3.1823

> open /Users/haandrew/Documents/progress/2026/Cryo-EM/scRibosome-
> twoSND1_merge_for_P2J138.pdb

Chain information for scRibosome-twoSND1_merge_for_P2J138.pdb #23  
---  
Chain | Description  
1 | No description available  
2 | No description available  
C1 | No description available  
C2 | No description available  
C3 | No description available  
C4 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LR | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LW | No description available  
LX | No description available  
LY | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Ld | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Lh | No description available  
Li | No description available  
Lj | No description available  
Lk | No description available  
Ll | No description available  
Lm | No description available  
Ln | No description available  
Lo | No description available  
Lp | No description available  
SA | No description available  
SB | No description available  
SC | No description available  
SD | No description available  
SE | No description available  
SF | No description available  
SG | No description available  
SH | No description available  
SI | No description available  
SJ | No description available  
SK | No description available  
SL | No description available  
SM | No description available  
SN | No description available  
SO | No description available  
SP | No description available  
SQ | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SU | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SY | No description available  
SZ | No description available  
Sa | No description available  
Sb | No description available  
Sc | No description available  
Sd | No description available  
Se | No description available  
Sf | No description available  
Sg | No description available  
s | No description available  
  

> open /Users/haandrew/Documents/progress/2026/Cryo-EM/scRibosome-
> twoSND1_merge_for_P2J138.pdb

Chain information for scRibosome-twoSND1_merge_for_P2J138.pdb #24  
---  
Chain | Description  
1 | No description available  
2 | No description available  
C1 | No description available  
C2 | No description available  
C3 | No description available  
C4 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LR | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LW | No description available  
LX | No description available  
LY | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Ld | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Lh | No description available  
Li | No description available  
Lj | No description available  
Lk | No description available  
Ll | No description available  
Lm | No description available  
Ln | No description available  
Lo | No description available  
Lp | No description available  
SA | No description available  
SB | No description available  
SC | No description available  
SD | No description available  
SE | No description available  
SF | No description available  
SG | No description available  
SH | No description available  
SI | No description available  
SJ | No description available  
SK | No description available  
SL | No description available  
SM | No description available  
SN | No description available  
SO | No description available  
SP | No description available  
SQ | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SU | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SY | No description available  
SZ | No description available  
Sa | No description available  
Sb | No description available  
Sc | No description available  
Sd | No description available  
Se | No description available  
Sf | No description available  
Sg | No description available  
s | No description available  
  

> hide #22 models

> select subtract #22

Nothing selected  

> hide #!23 models

> select add #24

205688 atoms, 220331 bonds, 17 pseudobonds, 17342 residues, 2 models selected  

> view matrix models #24,1,0,0,-47.345,0,1,0,-16.265,0,0,1,-284.06

> ui mousemode right ""rotate selected models""

> view matrix models
> #24,0.38469,0.75102,0.53665,-181.53,-0.8147,0.54956,-0.18508,287.88,-0.43392,-0.36601,0.82326,-80.021

> view matrix models
> #24,-0.97505,0.015931,-0.22143,418.67,-0.17847,-0.64944,0.73917,195.67,-0.13203,0.76025,0.63608,-331.01

> view matrix models
> #24,0.016709,0.84126,0.54037,-121.86,-0.69581,-0.37833,0.6105,279.15,0.71803,-0.3862,0.57903,-269.89

> view matrix models
> #24,-0.86869,0.49473,-0.024937,257.7,-0.092377,-0.11234,0.98937,15.836,0.48666,0.86176,0.14329,-378.34

> view matrix models
> #24,-0.77243,-0.10111,-0.627,485.54,-0.54131,-0.41155,0.73322,226.61,-0.33218,0.90576,0.26316,-237.86

> view matrix models
> #24,-0.99256,0.10607,-0.05974,369.75,-0.09536,-0.37242,0.92315,82.915,0.075669,0.92198,0.37976,-353.16

> view matrix models
> #24,-0.95953,-0.27399,-0.065004,440.24,-0.13242,0.23529,0.96286,-39.852,-0.24852,0.93251,-0.26205,-148.94

> select subtract #24

Nothing selected  

> select add #1

2 models selected  

> view matrix models
> #1,-0.90535,0.14613,-0.39873,421.82,0.18893,0.97949,-0.069999,-37.647,0.38032,-0.13871,-0.91439,341.68

> view matrix models
> #1,-0.82515,0.39791,0.40098,192.71,0.4908,0.85643,0.16011,-120.59,-0.27971,0.32892,-0.90199,378.49

> view matrix models
> #1,-0.258,0.8852,-0.3871,127.01,0.88631,0.057368,-0.45953,89.012,-0.38457,-0.46165,-0.79936,547.73

> view matrix models
> #1,-0.96477,0.093937,-0.24576,414.95,0.26309,0.3365,-0.90419,248.88,-0.0022395,-0.93699,-0.34936,478.92

> view matrix models
> #1,-0.20474,-0.92379,-0.32355,486.81,0.2983,0.25594,-0.91952,261.63,0.93226,-0.28477,0.22317,30.87

> view matrix models
> #1,0.75697,-0.63034,0.17224,124.37,0.38566,0.21818,-0.89647,246.73,0.52751,0.74503,0.40825,-139.38

> view matrix models
> #1,0.99549,-0.034587,0.08832,-35.315,0.094074,0.47895,-0.87279,247.89,-0.012114,0.87716,0.48005,-68.479

> view matrix models
> #1,0.94272,0.2833,0.17612,-109.1,0.021763,0.4746,-0.87993,265.39,-0.33287,0.83336,0.44125,15.79

> volume flip #1

Opened cryosparc_P1_J49_001_volume_map_sharp.mrc z flip as #25, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> select subtract #1

Nothing selected  

> select add #25

2 models selected  

> view matrix models
> #25,0.26615,0.91771,-0.2949,-0.94922,-0.63647,-0.062458,-0.76877,496.14,-0.72393,0.3923,0.56747,166.14

> surface dust #25 size 33.2

> view matrix models
> #25,-0.30131,0.88316,0.35949,-20.836,-0.70113,0.050305,-0.71125,472.94,-0.64624,-0.46636,0.60406,323.75

> view matrix models
> #25,0.27328,0.95867,0.079168,-94.72,-0.23202,0.14556,-0.96176,410.32,-0.93353,0.24446,0.26221,309.67

> view matrix models
> #25,0.94663,0.25102,-0.20221,-23.017,-0.11327,-0.32826,-0.93777,480.53,-0.30178,0.91062,-0.28231,157.59

> view matrix models
> #25,-0.25382,0.43303,0.86491,-48.29,0.96697,0.092183,0.23762,-97.85,0.023167,0.89665,-0.44213,128.11

> view matrix models
> #25,-0.14914,0.98041,-0.12863,35.703,0.78448,0.19651,0.5882,-160.04,0.60196,-0.013183,-0.79842,279.26

> view matrix models
> #25,0.23096,0.44593,-0.86476,233.81,0.75856,0.47406,0.44705,-181.91,0.6093,-0.75922,-0.22878,308.62

> view matrix models
> #25,0.95591,-0.0778,-0.28316,62.851,0.28693,0.042326,0.95701,-105.4,-0.062471,-0.99607,0.062783,434.58

> view matrix models
> #25,0.93594,-0.33771,-0.09979,81.175,0.12321,0.048597,0.99119,-80.033,-0.32989,-0.93999,0.087096,473.35

> hide #!25 models

> select subtract #25

Nothing selected  

> show #!1 models

> select add #1

2 models selected  

> view matrix models
> #1,0.99881,0.0028587,0.048629,-36.066,0.038894,0.55424,-0.83145,235.28,-0.029329,0.83235,0.55347,-69.955

> view matrix models
> #1,0.96872,0.22419,0.10643,-88.169,-0.035649,0.55012,-0.83432,252.36,-0.24559,0.80443,0.5409,-16.179

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.96872,0.22419,0.10643,-143.94,-0.035649,0.55012,-0.83432,262.05,-0.24559,0.80443,0.5409,-266.7

> view matrix models
> #1,0.96872,0.22419,0.10643,-504.82,-0.035649,0.55012,-0.83432,221.36,-0.24559,0.80443,0.5409,-165.02

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.81324,0.082368,-0.57607,-306.54,0.25323,-0.94138,0.22288,266.99,-0.52395,-0.32714,-0.78642,397.03

> view matrix models
> #1,-0.93493,-0.19574,-0.29595,63.437,0.34872,-0.35285,-0.86827,338.96,0.065525,-0.91498,0.39815,162.68

> select add #24

205688 atoms, 220331 bonds, 17 pseudobonds, 17342 residues, 4 models selected  

> select subtract #1

205688 atoms, 220331 bonds, 17 pseudobonds, 17342 residues, 2 models selected  

> view matrix models
> #24,-0.62219,0.43549,0.65056,72.683,0.65482,-0.16594,0.73735,-79.179,0.42906,0.88477,-0.18192,-301.2

> view matrix models
> #24,0.57832,-0.4931,0.64992,3.0833,-0.49957,-0.84387,-0.19572,503.03,0.64496,-0.21149,-0.73437,-8.892

> view matrix models
> #24,-0.52237,-0.56532,0.63839,255.21,-0.7069,0.70578,0.046568,183.97,-0.47689,-0.42695,-0.7683,281.34

> view matrix models
> #24,-0.96939,0.23301,0.077349,309.99,0.20616,0.94364,-0.25894,6.3294,-0.13333,-0.23506,-0.96279,210.9

> view matrix models
> #24,0.012267,0.99837,0.055722,-48.998,0.66549,-0.049744,0.74475,-106.41,0.7463,0.027947,-0.66502,-93.502

> view matrix models
> #24,0.59817,0.64144,0.48035,-193.08,0.014275,-0.60785,0.79392,134.44,0.80124,-0.46805,-0.37276,-67.922

> select subtract #24

Nothing selected  

> select add #1

2 models selected  

> view matrix models
> #1,0.64008,-0.70548,0.3043,-278.08,0.47923,0.057027,-0.87583,226.18,0.60053,0.70643,0.37459,-288.66

> view matrix models
> #1,0.75954,0.54606,0.35345,-578.28,0.35792,0.10286,-0.92807,252.28,-0.54313,0.83141,-0.11732,22.446

> view matrix models
> #1,-0.40351,0.91492,-0.010188,-340.31,0.30106,0.12225,-0.94574,263.61,-0.86403,-0.38468,-0.32477,388.83

> view matrix models
> #1,-0.11579,0.78119,-0.61346,-252.44,0.83268,-0.26037,-0.48873,142.44,-0.54152,-0.5674,-0.62033,418.66

> view matrix models
> #1,-0.97955,0.17307,-0.10263,-43.818,-0.11148,-0.89144,-0.43921,464.44,-0.16751,-0.41878,0.8925,8.1223

> view matrix models
> #1,-0.85026,0.462,-0.25222,-102.48,-0.34373,-0.85024,-0.39868,496.36,-0.39864,-0.25228,0.88173,23.435

> view matrix models
> #1,-0.44465,0.62583,-0.64081,-145.09,0.060262,-0.6929,-0.71851,441.81,-0.89368,-0.3581,0.27038,271.17

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.44465,0.62583,-0.64081,61.453,0.060262,-0.6929,-0.71851,463,-0.89368,-0.3581,0.27038,-26.983

> view matrix models
> #1,-0.44465,0.62583,-0.64081,293.85,0.060262,-0.6929,-0.71851,446.65,-0.89368,-0.3581,0.27038,103.73

> view matrix models
> #1,-0.44465,0.62583,-0.64081,263.76,0.060262,-0.6929,-0.71851,452.88,-0.89368,-0.3581,0.27038,121.44

Must specify one map, got 0  
Must specify one map, got 0  

> fitmap #1 inmodel #24

Expected a keyword  

> fitmap #24 inMap #1

Fit molecule scRibosome-twoSND1_merge_for_P2J138.pdb (#24) to map
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) using 205688 atoms  
average map value = 0.88, steps = 92  
shifted from previous position = 16.7  
rotated from previous position = 14.4 degrees  
atoms outside contour = 30417, contour level = 0.35186  
  
Position of scRibosome-twoSND1_merge_for_P2J138.pdb (#24) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99066496 0.13426151 -0.02359580 401.31992681  
0.13331980 0.99035331 0.03776419 -35.55227660  
0.02843846 0.03426587 -0.99900805 408.66727182  
Axis -0.06706868 -0.99758500 -0.01805412  
Axis point 199.18350637 0.00000000 207.27925730  
Rotation angle (degrees) 178.50555012  
Shift along axis 1.17229208  
  

> select subtract #1

Nothing selected  

> hide #!1 models

> show #!1 models

> volume #1 level 0.9412

> select add #1

2 models selected  

> view matrix models
> #1,-0.44465,0.62583,-0.64081,422.57,0.060262,-0.6929,-0.71851,239.24,-0.89368,-0.3581,0.27038,91.634

> view matrix models
> #1,-0.44465,0.62583,-0.64081,396.54,0.060262,-0.6929,-0.71851,411.62,-0.89368,-0.3581,0.27038,216.17

> view matrix models
> #1,-0.44465,0.62583,-0.64081,264.96,0.060262,-0.6929,-0.71851,447.21,-0.89368,-0.3581,0.27038,113.7

> fitmap #24 inMap #1

Fit molecule scRibosome-twoSND1_merge_for_P2J138.pdb (#24) to map
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) using 205688 atoms  
average map value = 0.88, steps = 60  
shifted from previous position = 9.67  
rotated from previous position = 0.0276 degrees  
atoms outside contour = 111402, contour level = 0.94121  
  
Position of scRibosome-twoSND1_merge_for_P2J138.pdb (#24) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99064266 0.13436821 -0.02392251 401.36483029  
0.13342491 0.99035186 0.03742938 -35.49783425  
0.02872103 0.03388728 -0.99901288 408.68500605  
Axis -0.06712206 -0.99758463 -0.01787539  
Axis point 199.17366828 0.00000000 207.31548317  
Rotation angle (degrees) 178.48804668  
Shift along axis 1.16625506  
  

> volume #1 level 0.461

> select subtract #1

Nothing selected  

> show #!23 models

> select add #24

205688 atoms, 220331 bonds, 17 pseudobonds, 17342 residues, 2 models selected  

> select subtract #24

Nothing selected  

> select add #23

205688 atoms, 220331 bonds, 17 pseudobonds, 17342 residues, 2 models selected  

> view matrix models #23,1,0,0,6.1177,0,1,0,145.1,0,0,1,-9.8481

> view matrix models #23,1,0,0,13.572,0,1,0,-78.83,0,0,1,-281.68

> view matrix models #23,1,0,0,296.63,0,1,0,-60.556,0,0,1,-116.11

> view matrix models #23,1,0,0,228.19,0,1,0,-419.6,0,0,1,-44.151

> view matrix models #23,1,0,0,-168.23,0,1,0,-245.53,0,0,1,-277.11

> view matrix models #23,1,0,0,-258.71,0,1,0,-365.84,0,0,1,-279.56

> ui mousemode right ""rotate selected models""

> view matrix models
> #23,0.85379,0.19423,0.48303,-369.7,-0.49522,0.016707,0.86861,-247.84,0.16064,-0.98081,0.11045,73.342

> ui mousemode right ""translate selected models""

> view matrix models
> #23,0.85379,0.19423,0.48303,-383.14,-0.49522,0.016707,0.86861,243.06,0.16064,-0.98081,0.11045,338.94

> view matrix models
> #23,0.85379,0.19423,0.48303,-193.15,-0.49522,0.016707,0.86861,152.79,0.16064,-0.98081,0.11045,370.48

> ui mousemode right ""rotate selected models""

> view matrix models
> #23,0.68856,0.2938,0.663,-216.32,-0.45243,-0.54047,0.70937,289.7,0.56674,-0.7884,-0.23922,319.72

> ui mousemode right ""translate selected models""

> view matrix models
> #23,0.68856,0.2938,0.663,-200.89,-0.45243,-0.54047,0.70937,241.45,0.56674,-0.7884,-0.23922,15.225

> fitmap #23 inMap #1

Fit molecule scRibosome-twoSND1_merge_for_P2J138.pdb (#23) to map
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) using 205688 atoms  
average map value = 0.88, steps = 140  
shifted from previous position = 30  
rotated from previous position = 25.2 degrees  
atoms outside contour = 41443, contour level = 0.461  
  
Position of scRibosome-twoSND1_merge_for_P2J138.pdb (#23) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99065654 0.13428559 -0.02381081 401.33628571  
0.13334686 0.99036335 0.03740292 -35.52823345  
0.02860401 0.03387835 -0.99901652 408.72103429  
Axis -0.06708154 -0.99758752 -0.01786641  
Axis point 199.17121351 0.00000000 207.32188921  
Rotation angle (degrees) 178.49462144  
Shift along axis 1.21789044  
  

> select subtract #23

Nothing selected  

> color zone #1 near #23

> hide #!24 models

> hide #!23 models

> color #1 #bfbebaff models

> show #!2 models

> select add #2

2 models selected  

> show #!3 models

> show #!4 models

> show #!5 models

> show #!7 models

> hide #!7 models

> hide #!4 models

> hide #!5 models

> hide #!3 models

> hide #!2 models

> volume #1 level 0.9958

> volume #2 level 0.9896

> volume #3 level 0.5326

> volume #4 level 0.6669

> volume #5 level 1.254

> volume #6 level 0.9946

> volume #7 level 1.297

> volume #8 level 1.036

> volume #9 level 1.595

> volume #10 level 1.044

> volume #11 level 1.112

> volume #14 level 0.6232

> volume #16 level 0.4208

> volume #17 level 0.9187

> volume #18 level 1.261

> volume #19 level 0.9165

> volume #19 level 0.878

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> select subtract #2

Nothing selected  

> hide #!25 models

> select add #2

2 models selected  

> view matrix models
> #2,0.60956,-0.76836,0.19511,501.52,-0.79273,-0.59228,0.14417,190.91,0.0047833,-0.24255,-0.97013,298.23

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.33071,0.52393,0.78494,158.34,-0.32262,-0.71886,0.61575,16.107,0.88687,-0.45688,-0.068703,-38.271

> view matrix models
> #2,0.21583,0.30389,0.92794,201.61,-0.24647,-0.9026,0.35293,94.313,0.94481,-0.30488,-0.11991,-73.397

> view matrix models
> #2,0.21588,0.304,0.92789,201.59,-0.24652,-0.90254,0.35305,94.282,0.94479,-0.30496,-0.1199,-73.379

> view matrix models
> #2,0.20489,0.2773,0.93868,207.56,-0.23594,-0.91676,0.32232,101.48,0.94992,-0.28752,-0.12241,-77.78

> view matrix models
> #2,0.24452,0.36822,0.89701,187.76,-0.27094,-0.86229,0.42783,75.257,0.93102,-0.34765,-0.11108,-62.899

> view matrix models
> #2,0.74017,0.22249,-0.63454,430.77,0.14714,-0.97439,-0.17002,132.62,-0.65612,0.032477,-0.75396,338.84

> view matrix models
> #2,0.76243,0.057781,-0.64448,463.79,-0.040989,-0.98969,-0.13722,170.56,-0.64577,0.13104,-0.7522,314.74

> view matrix models
> #2,0.73355,-0.20229,-0.64883,527.65,-0.33296,-0.93923,-0.083616,212.72,-0.59249,0.27737,-0.75632,272.02

> view matrix models
> #2,-0.15902,0.33589,-0.92838,665.83,-0.73531,-0.66778,-0.11566,249.06,-0.65881,0.66426,0.35317,-29.775

> view matrix models
> #2,-0.55938,0.59127,-0.58095,625.8,-0.11148,-0.74815,-0.6541,241.73,-0.82138,-0.30112,0.48441,188.66

> view matrix models
> #2,-0.5595,0.58136,-0.59075,630.04,-0.11041,-0.75867,-0.64205,241.26,-0.82144,-0.294,0.48866,186.23

> view matrix models
> #2,-0.55945,0.58506,-0.58712,628.46,-0.11081,-0.75478,-0.64655,241.44,-0.82142,-0.29666,0.4871,187.13

> view matrix models
> #2,-0.50031,0.6501,-0.57189,598.08,-0.23282,-0.73718,-0.63432,261.95,-0.83396,-0.18421,0.52017,158.5

> ui mousemode right ""move picked models""

> view matrix models
> #2,-0.50031,0.6501,-0.57189,380.81,-0.23282,-0.73718,-0.63432,528.29,-0.83396,-0.18421,0.52017,252.86

> view matrix models
> #2,-0.50031,0.6501,-0.57189,247.33,-0.23282,-0.73718,-0.63432,511.92,-0.83396,-0.18421,0.52017,23.275

> fitmap #2 inMap #1

Fit map cryosparc_P1_J49_001_volume_map.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 23497 points  
correlation = 0.9913, correlation about mean = 0.8492, overlap = 5.084e+04  
steps = 120, shift = 20, angle = 18.2 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#2) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999995 -0.00020371 -0.00032536 0.14476519  
0.00020362 0.99999997 -0.00026248 0.03803555  
0.00032541 0.00026241 0.99999993 -0.14702941  
Axis 0.56438844 -0.69974138 0.43798137  
Axis point 439.42587188 0.00000000 460.99015298  
Rotation angle (degrees) 0.02664276  
Shift along axis -0.00930739  
  

> select subtract #2

Nothing selected  

> show #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> select add #3

2 models selected  

> view matrix models
> #3,-0.81182,0.4742,-0.3407,454.52,-0.17891,0.35341,0.9182,-301.5,0.55582,0.80637,-0.20207,-63.972

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,0.19406,0.16832,0.96644,26.561,0.97847,0.037388,-0.20299,-237.31,-0.0703,0.98502,-0.15744,20.439

> view matrix models
> #3,-0.51197,-0.35704,0.78129,329.39,0.75379,0.24943,0.60794,-409.87,-0.41193,0.90017,0.14143,46.874

> view matrix models
> #3,-0.85847,0.48596,-0.16395,423.86,0.40617,0.83938,0.36122,-410.66,0.31315,0.2435,-0.91796,262.93

> view matrix models
> #3,0.036545,0.96106,0.27391,37.532,0.96105,0.041334,-0.27325,-219.37,-0.27393,0.27323,-0.92212,381.73

> view matrix models
> #3,-0.13839,0.72479,0.67492,39.416,0.91497,-0.16725,0.36722,-302.23,0.37905,0.66836,-0.64002,97.433

> ui mousemode right ""translate selected models""

> view matrix models
> #3,-0.13839,0.72479,0.67492,-94.61,0.91497,-0.16725,0.36722,164.16,0.37905,0.66836,-0.64002,79.595

> view matrix models
> #3,-0.13839,0.72479,0.67492,-223.18,0.91497,-0.16725,0.36722,207.25,0.37905,0.66836,-0.64002,-52.851

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,-0.25418,0.73602,0.62743,-190.87,0.83284,-0.16324,0.52889,189.03,0.4917,0.65699,-0.57149,-88.984

> view matrix models
> #3,0.24566,0.96936,-0.0012755,-211.99,0.4433,-0.11117,0.88945,182.76,0.86205,-0.21907,-0.45703,-2.7602

> ui mousemode right ""move picked models""

> view matrix models
> #3,0.24566,0.96936,-0.0012755,-107.32,0.4433,-0.11117,0.88945,-91.296,0.86205,-0.21907,-0.45703,-144.39

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!4 models

> ui mousemode right ""rotate selected models""

> select add #4

2 models selected  

> view matrix models
> #4,0.71459,-0.64679,-0.2665,260.74,0.30768,-0.051541,0.95009,-42.751,-0.62824,-0.76093,0.16218,483.61

> view matrix models
> #4,-0.47693,0.7383,-0.47693,262.65,-0.85078,-0.25153,0.46141,358.06,0.2207,0.62582,0.74809,-130.02

> view matrix models
> #4,-0.98658,-0.15677,-0.045656,475.37,0.10578,-0.40062,-0.91012,479.49,0.12439,-0.90273,0.41183,297.18

> view matrix models
> #4,-0.96149,0.26933,-0.054782,378.91,-0.1289,-0.61791,-0.77561,548.78,-0.24275,-0.73868,0.62883,294.16

> view matrix models
> #4,-0.98293,-0.13744,-0.12228,486.93,0.13091,-0.055573,-0.98984,415.97,0.12924,-0.98895,0.072617,388.29

> volume #4 level 0.445

> view matrix models
> #4,-0.95856,-0.19407,-0.20855,514.25,0.20861,0.02038,-0.97779,380.3,0.19401,-0.98078,0.020949,384.94

> view matrix models
> #4,0.82621,0.21936,0.5189,-117.48,-0.12815,-0.82376,0.55227,281.39,0.54859,-0.52279,-0.65249,366.44

> view matrix models
> #4,0.20859,0.56612,-0.79749,240.27,0.94577,-0.32438,0.017104,71.625,-0.24901,-0.75781,-0.60309,573.04

> view matrix models
> #4,-0.97879,-0.020749,-0.20382,479.36,0.19302,-0.42688,-0.88347,459.82,-0.068677,-0.90407,0.42183,330.1

> view matrix models
> #4,-0.97741,-0.14598,-0.15287,494.74,0.17364,-0.14212,-0.9745,422.49,0.12054,-0.97902,0.16426,366.7

> ui mousemode right ""translate selected models""

> view matrix models
> #4,-0.97741,-0.14598,-0.15287,378.24,0.17364,-0.14212,-0.9745,451.95,0.12054,-0.97902,0.16426,99.337

> view matrix models
> #4,-0.97741,-0.14598,-0.15287,410.06,0.17364,-0.14212,-0.9745,361.63,0.12054,-0.97902,0.16426,54.573

> hide #!4 models

> select subtract #4

Nothing selected  

> show #!5 models

> select add #5

2 models selected  

> view matrix models
> #5,0.94884,0.21626,0.23005,-269.88,-0.16928,0.96347,-0.20754,279.73,-0.26653,0.15798,0.95079,-90.569

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,-0.44586,-0.32097,0.83557,3.6126,-0.64601,0.76155,-0.052174,387.95,-0.61958,-0.56305,-0.5469,450.12

> view matrix models
> #5,-0.76512,-0.086479,0.63806,63.943,0.48487,0.57464,0.65931,39.004,-0.42367,0.81383,-0.39773,93.615

> ui mousemode right ""translate selected models""

> view matrix models
> #5,-0.76512,-0.086479,0.63806,200.21,0.48487,0.57464,0.65931,-205.78,-0.42367,0.81383,-0.39773,-92.572

> fitmap #2 inMap #1

Fit map cryosparc_P1_J49_001_volume_map.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 23497 points  
correlation = 0.9911, correlation about mean = 0.8469, overlap = 5.107e+04  
steps = 36, shift = 0.0443, angle = 0.0237 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#2) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00021951 -0.00008997 0.06408117  
0.00021951 0.99999999 0.00007828 -0.06929975  
0.00008995 -0.00007830 1.00000001 -0.02395475  
Axis -0.31338734 -0.36009777 0.87870244  
Axis point 342.26518886 268.79245294 0.00000000  
Rotation angle (degrees) 0.01431322  
Shift along axis -0.01617664  
  

> fitmap #3 inMap #1

Fit map cryosparc_P1_J97_002_volume_map_sharp.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 56198 points  
correlation = 0.5786, correlation about mean = 0.03341, overlap = 1.661e+04  
steps = 152, shift = 18.5, angle = 15.1 degrees  
  
Position of cryosparc_P1_J97_002_volume_map_sharp.mrc (#3) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.87979777 -0.34466184 0.32735926 407.44281122  
-0.43817443 0.85500994 -0.27741875 183.79832786  
-0.18427977 -0.38751286 -0.90325785 534.81482134  
Axis -0.20708441 0.96238090 -0.17589498  
Axis point 261.08369443 0.00000000 255.57628817  
Rotation angle (degrees) 164.58435252  
Shift along axis -1.56229845  
  

> fitmap #4 inMap #1

Fit map cryosparc_P1_J97_002_volume_map.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 78366 points  
correlation = 0.5652, correlation about mean = 0.06789, overlap = 2.024e+04  
steps = 144, shift = 26.6, angle = 14.2 degrees  
  
Position of cryosparc_P1_J97_002_volume_map.mrc (#4) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46898217 0.88131733 0.05775364 -73.54777001  
-0.79252681 0.39106890 0.46793842 203.57879115  
0.38981659 -0.26522608 0.88187195 7.18313422  
Axis -0.39474823 -0.17878834 -0.90122614  
Axis point 126.36767626 165.79033932 0.00000000  
Rotation angle (degrees) 68.22507164  
Shift along axis -13.83828953  
  

> fitmap #5 inMap #1

Fit map cryosparc_P1_J98_001_volume_map_sharp.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 15013 points  
correlation = 0.6197, correlation about mean = 0.04936, overlap = 1.153e+04  
steps = 88, shift = 13.6, angle = 10.1 degrees  
  
Position of cryosparc_P1_J98_001_volume_map_sharp.mrc (#5) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.81731865 -0.54494787 0.18714172 121.60855897  
-0.55683584 -0.83051286 0.01349835 504.24650714  
0.14806770 -0.11523967 -0.98224017 411.79027378  
Axis -0.95318149 0.28930554 -0.08801903  
Axis point 0.00000000 277.87043769 191.30673445  
Rotation angle (degrees) 176.12782894  
Shift along axis -6.27909781  
  

> volume #5 level 1.188

> hide #!5 models

> select subtract #5

Nothing selected  

> show #!6 models

> ui mousemode right ""rotate selected models""

> select add #6

2 models selected  

> view matrix models
> #6,0.90257,-0.41067,-0.12934,132.18,0.07275,0.44154,-0.89429,289.66,0.42436,0.79774,0.42839,-130.87

> view matrix models
> #6,-0.85783,-0.44324,0.26011,421.16,-0.27693,0.82503,0.49258,-11.114,-0.43293,0.35052,-0.83048,406.06

> view matrix models
> #6,-0.86753,-0.053706,0.49448,293.25,0.30129,0.73426,0.60834,-136.86,-0.39575,0.67674,-0.62082,286.71

> view matrix models
> #6,-0.95166,-0.041373,0.30437,348.5,0.2678,0.37355,0.88811,-115.05,-0.15044,0.92669,-0.34441,125.75

> volume #6 level 0.7556

> ui mousemode right ""translate selected models""

> view matrix models
> #6,-0.95166,-0.041373,0.30437,456.4,0.2678,0.37355,0.88811,-189.89,-0.15044,0.92669,-0.34441,-70.403

> view matrix models
> #6,-0.95166,-0.041373,0.30437,317.78,0.2678,0.37355,0.88811,-156.3,-0.15044,0.92669,-0.34441,-187.06

> hide #!6 models

> show #!21 models

> show #!20 models

> show #!19 models

> show #!18 models

> show #!17 models

> show #!16 models

> show #!15 models

> show #!14 models

> select add #14

4 models selected  

> select add #15

6 models selected  

> select add #16

8 models selected  

> select add #17

10 models selected  

> select add #18

12 models selected  

> select add #19

14 models selected  

> select add #20

16 models selected  

> select add #21

18 models selected  

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> hide #!14 models

> ui mousemode right ""rotate selected models""

> view matrix models
> #6,-0.88863,-0.35545,0.28981,466.04,-0.068651,0.72789,0.68225,-248.5,-0.45346,0.58637,-0.67123,78.622,#14,-0.79261,0.43289,0.4294,172.45,0.39433,0.90107,-0.18051,-43.826,-0.46506,0.026247,-0.88489,481.71,#15,-0.79258,0.43287,0.42947,172.43,0.39437,0.90107,-0.18041,-43.883,-0.46508,0.026384,-0.88488,481.71,#16,-0.7966,0.37665,0.47283,178.01,0.30847,0.92594,-0.21789,-22.874,-0.51988,-0.027716,-0.85379,496.84,#17,-0.79683,0.37661,0.47247,178.13,0.30835,0.92595,-0.21805,-22.841,-0.5196,-0.028065,-0.85395,496.9,#18,-0.74248,0.48064,0.46659,145.92,0.40785,0.87692,-0.25432,-25.385,-0.53139,0.0014652,-0.84712,493.46,#19,-0.74263,0.48026,0.46675,146,0.4075,0.87713,-0.25415,-25.399,-0.53146,0.0014656,-0.84708,493.45,#20,0.059324,-0.97133,0.23022,341.19,0.80043,0.1841,0.57045,-134.36,-0.59648,0.15044,0.7884,119.57,#21,0.059493,-0.97129,0.23035,341.13,0.80047,0.18429,0.57034,-134.43,-0.59642,0.15045,0.78845,119.55

> view matrix models
> #6,-0.27537,0.061818,-0.95935,327.62,-0.81741,0.51018,0.2675,42.66,0.50597,0.85785,-0.089956,-297.6,#14,-0.56346,-0.53499,-0.62952,547.48,-0.48092,0.83199,-0.27661,182.35,0.67174,0.14689,-0.72608,174.33,#15,-0.5635,-0.53488,-0.62958,547.51,-0.48088,0.83205,-0.27649,182.3,0.67173,0.14695,-0.72608,174.31,#16,-0.55667,-0.59002,-0.58481,546.97,-0.56265,0.7857,-0.25712,206.01,0.61119,0.18591,-0.76934,186.11,#17,-0.55636,-0.5903,-0.58482,546.99,-0.56273,0.7855,-0.25752,206.13,0.61139,0.18582,-0.7692,186.05,#18,-0.62762,-0.54332,-0.55758,547.51,-0.47399,0.83484,-0.27996,182.84,0.6176,0.088575,-0.78149,208.7,#19,-0.62746,-0.54342,-0.55766,547.5,-0.47432,0.83473,-0.27973,182.88,0.61751,0.088988,-0.78151,208.63,#20,-0.95623,0.066098,0.28506,300.07,0.23274,-0.41866,0.87781,54.633,0.17737,0.90573,0.38495,-126.17,#21,-0.95621,0.065993,0.28516,300.1,0.2329,-0.41851,0.87784,54.543,0.17727,0.90581,0.38481,-126.16

> view matrix models
> #6,0.6015,0.44356,-0.66442,-50.318,-0.62157,0.78231,-0.040438,-83.433,0.50185,0.43731,0.74627,-202.41,#14,0.43201,-0.52635,-0.73234,348.95,-0.33465,0.6605,-0.67213,268.59,0.83748,0.53544,0.1092,-117.32,#15,0.43197,-0.52628,-0.73242,348.97,-0.33463,0.6606,-0.67203,268.54,0.83751,0.53539,0.10925,-117.36,#16,0.42653,-0.50425,-0.75087,346.98,-0.42797,0.61884,-0.65869,293.9,0.79682,0.6023,0.048154,-109.99,#17,0.42688,-0.50437,-0.75059,346.9,-0.42789,0.61857,-0.659,294,0.79667,0.60248,0.04824,-110.04,#18,0.3566,-0.57519,-0.7362,374.34,-0.36451,0.63989,-0.67651,281.42,0.86021,0.5096,0.018522,-98.028,#19,0.35676,-0.57489,-0.73636,374.27,-0.3648,0.63992,-0.67633,281.42,0.86003,0.50991,0.018579,-98.062,#20,-0.4484,0.89294,0.039979,58.278,0.025513,-0.031923,0.99916,-18.06,0.89347,0.44905,-0.0084671,-83.148,#21,-0.44853,0.89288,0.039909,58.335,0.025626,-0.031787,0.99917,-18.131,0.8934,0.44918,-0.0086234,-83.169

> volume #15 level 0.723

> ui mousemode right ""translate selected models""

> view matrix models
> #6,0.6015,0.44356,-0.66442,40.545,-0.62157,0.78231,-0.040438,-173.99,0.50185,0.43731,0.74627,-400.35,#14,0.43201,-0.52635,-0.73234,439.81,-0.33465,0.6605,-0.67213,178.03,0.83748,0.53544,0.1092,-315.26,#15,0.43197,-0.52628,-0.73242,439.83,-0.33463,0.6606,-0.67203,177.98,0.83751,0.53539,0.10925,-315.29,#16,0.42653,-0.50425,-0.75087,437.84,-0.42797,0.61884,-0.65869,203.34,0.79682,0.6023,0.048154,-307.92,#17,0.42688,-0.50437,-0.75059,437.76,-0.42789,0.61857,-0.659,203.44,0.79667,0.60248,0.04824,-307.97,#18,0.3566,-0.57519,-0.7362,465.2,-0.36451,0.63989,-0.67651,190.86,0.86021,0.5096,0.018522,-295.96,#19,0.35676,-0.57489,-0.73636,465.13,-0.3648,0.63992,-0.67633,190.86,0.86003,0.50991,0.018579,-296,#20,-0.4484,0.89294,0.039979,149.14,0.025513,-0.031923,0.99916,-108.62,0.89347,0.44905,-0.0084671,-281.08,#21,-0.44853,0.89288,0.039909,149.2,0.025626,-0.031787,0.99917,-108.69,0.8934,0.44918,-0.0086234,-281.1

> view matrix models
> #6,0.6015,0.44356,-0.66442,-42.139,-0.62157,0.78231,-0.040438,-120.02,0.50185,0.43731,0.74627,-488.42,#14,0.43201,-0.52635,-0.73234,357.13,-0.33465,0.6605,-0.67213,232,0.83748,0.53544,0.1092,-403.33,#15,0.43197,-0.52628,-0.73242,357.15,-0.33463,0.6606,-0.67203,231.96,0.83751,0.53539,0.10925,-403.36,#16,0.42653,-0.50425,-0.75087,355.16,-0.42797,0.61884,-0.65869,257.32,0.79682,0.6023,0.048154,-395.99,#17,0.42688,-0.50437,-0.75059,355.07,-0.42789,0.61857,-0.659,257.41,0.79667,0.60248,0.04824,-396.04,#18,0.3566,-0.57519,-0.7362,382.52,-0.36451,0.63989,-0.67651,244.83,0.86021,0.5096,0.018522,-384.03,#19,0.35676,-0.57489,-0.73636,382.45,-0.3648,0.63992,-0.67633,244.83,0.86003,0.50991,0.018579,-384.06,#20,-0.4484,0.89294,0.039979,66.457,0.025513,-0.031923,0.99916,-54.646,0.89347,0.44905,-0.0084671,-369.15,#21,-0.44853,0.89288,0.039909,66.514,0.025626,-0.031787,0.99917,-54.717,0.8934,0.44918,-0.0086234,-369.17

> fitmap #21 inMap #1

Fit map cryosparc_P1_J108_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 50668 points  
correlation = 0.9363, correlation about mean = 0.5931, overlap = 4.442e+04  
steps = 116, shift = 10.6, angle = 15.6 degrees  
  
Position of cryosparc_P1_J108_001_volume_map.mrc z flip (#21) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.69722091 -0.66681163 0.26314484 446.15123279  
-0.64056974 0.41474667 -0.64626276 393.21069291  
0.32179709 -0.61915055 -0.71630942 437.70886650  
Axis 0.38875619 -0.84100200 0.37627683  
Axis point 309.44766119 0.00000000 311.41465143  
Rotation angle (degrees) 178.00166477  
Shift along axis 7.45278003  
  

> fitmap #20 inMap #1

Fit map cryosparc_P1_J108_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20960 points  
correlation = 0.9607, correlation about mean = 0.5066, overlap = 3.58e+04  
steps = 100, shift = 8.98, angle = 15.6 degrees  
  
Position of cryosparc_P1_J108_001_volume_map_sharp.mrc z flip (#20) relative
to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.69735507 -0.66659148 0.26334711 446.11538956  
-0.64075788 0.41520272 -0.64578327 393.12728635  
0.32113119 -0.61908197 -0.71666746 437.90594299  
Axis 0.38867981 -0.84113914 0.37604914  
Axis point 309.44378721 0.00000000 311.35730259  
Rotation angle (degrees) 178.03157705  
Shift along axis 7.39545109  
  

> fitmap #19 inMap #1

Fit map cryosparc_P1_J104_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 31946 points  
correlation = 0.9726, correlation about mean = 0.6536, overlap = 4.68e+04  
steps = 112, shift = 13.1, angle = 15.6 degrees  
  
Position of cryosparc_P1_J104_001_volume_map.mrc z flip (#19) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98937200 -0.14536553 0.00344927 453.78968015  
0.14529255 -0.98925754 -0.01611153 396.24423525  
0.00575427 -0.01543915 0.99986424 2.15653353  
Axis 0.00231325 -0.00793004 0.99996588  
Axis point 212.41805692 214.70699134 0.00000000  
Rotation angle (degrees) 171.64337919  
Shift along axis 0.06395459  
  

> fitmap #18 inMap #1

Fit map cryosparc_P1_J104_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 25838 points  
correlation = 0.9686, correlation about mean = 0.5898, overlap = 5.954e+04  
steps = 100, shift = 12.7, angle = 15.6 degrees  
  
Position of cryosparc_P1_J104_001_volume_map_sharp.mrc z flip (#18) relative
to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98947804 -0.14464737 0.00321708 453.69601027  
0.14458044 -0.98936883 -0.01567800 396.25026367  
0.00545066 -0.01504791 0.99987191 2.14304979  
Axis 0.00217846 -0.00772232 0.99996781  
Axis point 212.44320093 214.62382300 0.00000000  
Rotation angle (degrees) 171.68480854  
Shift along axis 0.07136871  
  

> fitmap #17 inMap #1

Fit map cryosparc_P1_J103_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 29219 points  
correlation = 0.9806, correlation about mean = 0.6608, overlap = 4.488e+04  
steps = 112, shift = 13.1, angle = 15.6 degrees  
  
Position of cryosparc_P1_J103_001_volume_map.mrc z flip (#17) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96680237 -0.25502082 -0.01604854 475.63744719  
0.25550434 -0.96561874 -0.04793720 375.10677453  
-0.00327179 -0.05044627 0.99872141 13.30973048  
Axis -0.00491309 -0.02501855 0.99967491  
Axis point 213.49188633 218.60521419 0.00000000  
Rotation angle (degrees) 165.20593606  
Shift along axis 1.58392768  
  

> fitmap #16 inMap #1

Fit map cryosparc_P1_J103_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 83702 points  
correlation = 0.9443, correlation about mean = 0.7798, overlap = 8.775e+04  
steps = 112, shift = 15.1, angle = 15.6 degrees  
  
Position of cryosparc_P1_J103_001_volume_map_sharp.mrc z flip (#16) relative
to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96685076 -0.25484220 -0.01597028 475.59698170  
0.25532241 -0.96566039 -0.04806728 375.14545317  
-0.00317229 -0.05055146 0.99871641 13.35686200  
Axis -0.00486777 -0.02507780 0.99967365  
Axis point 213.48660701 218.60044325 0.00000000  
Rotation angle (degrees) 165.21660343  
Shift along axis 1.62958078  
  

> fitmap #15 inMap #1

Fit map cryosparc_P1_J98_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 37686 points  
correlation = 0.941, correlation about mean = 0.482, overlap = 4.055e+04  
steps = 92, shift = 13.8, angle = 15.6 degrees  
  
Position of cryosparc_P1_J98_001_volume_map.mrc z flip (#15) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98115626 -0.17548487 -0.08085450 474.87934814  
0.17989885 -0.98236532 -0.05093882 396.45924831  
-0.07048966 -0.06452457 0.99542341 29.22298152  
Axis -0.03818429 -0.02913154 0.99884599  
Axis point 220.20435859 219.96923969 0.00000000  
Rotation angle (degrees) 169.75270090  
Shift along axis -0.49313815  
  

> fitmap #14 inMap #1

Fit map cryosparc_P1_J98_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 57626 points  
correlation = 0.9156, correlation about mean = 0.5549, overlap = 5.979e+04  
steps = 108, shift = 14.7, angle = 15.6 degrees  
  
Position of cryosparc_P1_J98_001_volume_map_sharp.mrc z flip (#14) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98115541 -0.17563607 -0.08053577 474.88496525  
0.18003760 -0.98233398 -0.05105281 396.45902867  
-0.07014630 -0.06459020 0.99544341 29.15850208  
Axis -0.03801754 -0.02917709 0.99885102  
Axis point 220.18894103 219.98655737 0.00000000  
Rotation angle (degrees) 169.74430222  
Shift along axis -0.49648181  
  

> select subtract #21

16 models selected  

> select subtract #20

14 models selected  

> select subtract #19

12 models selected  

> select subtract #18

10 models selected  

> select subtract #17

8 models selected  

> select subtract #16

6 models selected  

> select subtract #15

4 models selected  

> select subtract #14

2 models selected  

> show #!16 models

> hide #!16 models

> volume #1 level 0.1227

> hide #!1 models

> volume #1 level 0.4283

> volresample #14 ongrid #1

Unknown command: volresample #14 ongrid #1  

> volume resample #14 onGrid #1

Opened cryosparc_P1_J98_001_volume_map_sharp.mrc z flip resampled as #26, grid
size 128,128,128, pixel 3.32, shown at step 1, values float32  

> volume resample #3 onGrid #1

Opened cryosparc_P1_J97_002_volume_map_sharp.mrc resampled as #27, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> hide #!27 models

> volume resample #16 onGrid #1

Opened cryosparc_P1_J103_001_volume_map_sharp.mrc z flip resampled as #28,
grid size 128,128,128, pixel 3.32, shown at step 1, values float32  

> show #!20 models

> volume #20 level 0.5538

> surface dust #1 size 33.2

> surface dust #15 size 33.2

> surface dust #20 size 33.2

> surface dust #26 size 33.2

> surface dust #28 size 33.2

> volume resample #20 onGrid #1

Opened cryosparc_P1_J108_001_volume_map_sharp.mrc z flip resampled as #29,
grid size 128,128,128, pixel 3.32, shown at step 1, values float32  

> volume morph #26-30

Opened morph as #30, grid size 128,128,128, pixel 3.32, shown at step 1,
values float32  

> select subtract #6

Nothing selected  

> hide #!30 models

> hide #!15 models

> volume #1 level 0.2209

> volume #1 level 0.3082

> hide #!1 models

> show #!26 models

> volume #26 level 0.1946

> volume #26 level 0.2335

> volume #27 level 0.4201

> hide #!27 models

> volume #28 level 0.1795

> show #!29 models

> hide #!28 models

> hide #!26 models

> volume #29 level 0.4606

> surface dust #29 size 33.2

> volume #29 level 0.4199

> show #!18 models

> volume resample #18 onGrid #1

Opened cryosparc_P1_J104_001_volume_map_sharp.mrc z flip resampled as #31,
grid size 128,128,128, pixel 3.32, shown at step 1, values float32  

> volume #31 level 0.4527

> volume morph #1,26,28,29,31

Opened morph as #32, grid size 128,128,128, pixel 3.32, shown at step 1,
values float32  

> surface dust #32 size 33.2

> show #!1 models

> hide #!1 models

> color #32 #d0dcd0ff models

> color #32 #dadccaff models

> color #32 #8d8e82ff models

> color #32 #8d8f83ff models

> color #32 #919191ff models

> color #32 #797979ff models

> volume #32 level 0.2864

> volume #32 color #e9e9c7

> volume #32 color #fbb5fb

> volume #32 style image

> volume #32 style surface

> volume #32 style mesh

> volume #32 style image maximumIntensityProjection true

> volume #32 region 0,0,63,127,127,63 step 1 maximumIntensityProjection false
> showOutlineBox true

> volume #32 region 0,0,0,127,127,127 step 1

> volume #32 region 0,0,0,127,127,127 step 1 colorMode opaque8 orthoplanes xyz
> positionPlanes 63,63,63 imageMode orthoplanes

> volume #32 imageMode ""box faces""

> volume #32 style surface

> volume #32

> volume #32 style image

> volume #32 style surface

> volume #!32 showOutlineBox false


===== Log before crash end =====

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: Z11D000L9D/A
      Chip: Unknown
      Total Number of Cores: 8 (4 Performance and 4 Efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 13822.81.10

Software:

    System Software Overview:

      System Version: macOS 26.3 (25D125)
      Kernel Version: Darwin 25.3.0
      Time since boot: 45 days, 18 hours, 47 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2722H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	new	normal		Unassigned