![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 hours ago
Closed 104 minutes ago
#20360 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Current thread 0x00000002009f9e40 (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.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 61)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 110469,
"osVersion" : {
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"build" : "25D125",
"releaseType" : "User"
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"captureTime" : "2026-05-19 17:12:39.3276 +0200",
"codeSigningMonitor" : 1,
"incident" : "E669E62F-2318-4813-B5D1-CF12B38F1FD5",
"pid" : 29390,
"translated" : true,
"cpuType" : "X86-64",
"procLaunch" : "2026-05-19 13:59:33.6676 +0200",
"procStartAbsTime" : 16802689782557,
"procExitAbsTime" : 17080677442298,
"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" : 18730,
"sleepWakeUUID" : "97C9ADF8-79FC-49D9-9F88-793BF4D3857D",
"sip" : "disabled",
"vmRegionInfo" : "0x326f00bf4d18 is not in any region. Bytes after previous region: 54971298958617 Bytes before following region: 50100780970728\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, 0x0000b26f00bf4d18","rawCodes":[1,196189823651096],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000b26f00bf4d18 -> 0x0000326f00bf4d18 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":29390},
"vmregioninfo" : "0x326f00bf4d18 is not in any region. Bytes after previous region: 54971298958617 Bytes before following region: 50100780970728\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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"name" : "_frame.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6064848896,
"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" : 6024327168,
"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" : 6065684480,
"size" : 98304,
"uuid" : "ae16bb51-bedf-3c8a-9b96-5684b608789d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6743347200,
"size" : 524288,
"uuid" : "58e1300b-c472-3863-8fc4-4eb27185cbbf",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6747639808,
"size" : 442368,
"uuid" : "9141612b-bf67-390f-8b66-18a585729cab",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6070009856,
"size" : 180224,
"uuid" : "6d0a4aa1-f80b-3e16-baed-3f694111a75d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6713376768,
"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" : 5992767488,
"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"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6027214848,
"size" : 49152,
"uuid" : "e85fa1ce-f4e4-3454-9368-bd7d363c7e9e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/iconengines\/libqsvgicon.dylib",
"name" : "libqsvgicon.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
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"arch" : "x86_64",
"base" : 140703409131520,
"size" : 252184,
"uuid" : "62e8ef56-067e-397a-be4f-6cc00881a2ee",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
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"arch" : "x86_64",
"base" : 140703409385472,
"size" : 49192,
"uuid" : "f9c81fc7-1abf-3b5e-a6b3-3113dad29577",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
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"base" : 140703407898624,
"size" : 563448,
"uuid" : "b349e7c1-a14b-3991-b786-dbba5ee9d443",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
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"size" : 40016,
"uuid" : "fc0c42b2-0b55-370b-8fc7-17bac96bb458",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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{
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"base" : 140703474651136,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 25138887,
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"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
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"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 5549334,
"uuid" : "c4a0ebe2-9423-327e-8969-0d1873b3c7d8",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
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"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4956771,
"uuid" : "0dec7be2-3fd1-3ac1-9f83-7d1333f68ec3",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "4302"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703625371648,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3007016,
"uuid" : "a50fbb92-900e-3d92-9ae8-49e3693fbbcb",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
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"size" : 566416,
"uuid" : "fad5093a-e81d-3a83-aabc-c23b2fa28ebe",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
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"size" : 30064771072,
"uuid" : "21e21a13-985d-34f6-bfe0-1fd3ff38209f"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "2c9da79f9f95f1e554267120f42823b53c71704c",
"bug_type" : "309",
"roots_installed" : 0,
"trmStatus" : 1,
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : [
],
"deploymentId" : 240000025
},
{
"rolloutId" : "6434420a89ec2e0a7a38bf5a",
"factorPackIds" : [
],
"deploymentId" : 240000011
}
],
"experiments" : [
]
},
"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/Downloads/cryosparc_P3_J51_002_volume_map(1).mrc
> /Users/haandrew/Downloads/cryosparc_P3_J50_002_volume_map_sharp.mrc
> /Users/haandrew/Downloads/cryosparc_P3_J50_002_volume_map.mrc
> /Users/haandrew/Downloads/cryosparc_P3_J51_002_volume_map_sharp.mrc
> /Users/haandrew/Downloads/cryosparc_P3_J51_002_volume_map.mrc
Opened cryosparc_P3_J51_002_volume_map(1).mrc as #1.1, grid size 128,128,128,
pixel 3.35, shown at level 1.28, step 1, values float32
Opened cryosparc_P3_J50_002_volume_map_sharp.mrc as #1.2, grid size
128,128,128, pixel 3.35, shown at level 1.89, step 1, values float32
Opened cryosparc_P3_J50_002_volume_map.mrc as #1.3, grid size 128,128,128,
pixel 3.35, shown at level 1.29, step 1, values float32
Opened cryosparc_P3_J51_002_volume_map_sharp.mrc as #1.4, grid size
128,128,128, pixel 3.35, shown at level 1.89, step 1, values float32
Opened cryosparc_P3_J51_002_volume_map.mrc as #1.5, grid size 128,128,128,
pixel 3.35, shown at level 1.28, step 1, values float32
> hide #!1 models
> open "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39
> and exit focus mask /NU/cryosparc_P1_J49_001_volume_map_sharp.mrc"
> "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39 and
> exit focus mask /NU/cryosparc_P1_J49_001_volume_map.mrc"
Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #2.1, grid size
128,128,128, pixel 3.32, shown at level 1.35, step 1, values float32
Opened cryosparc_P1_J49_001_volume_map.mrc as #2.2, 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/Stm1 mask 2.mrc"
Opened Stm1 mask 2.mrc as #3, grid size 128,128,128, pixel 3.32, shown at
level 0.0871, step 1, values float32
> color #2.2 #919191ff models
> hide #!2.2 models
> volume #3 level 0.362
> hide #!2.1 models
> show #!2.1 models
> color #2.1 #919191ff models
> volume #2.2 level 0.4564
> volume #3 color #e5bf996b
> ui tool show "Side View"
> ui mousemode right "map eraser"
> close session
> open "/Users/haandrew/Documents/progress/2026/Cryo-EM/Stm1 apo study.cxs"
Opened cryosparc_P3_J50_002_volume_map_sharp.mrc as #1, grid size 128,128,128,
pixel 3.35, shown at level 0.687, step 1, values float32
Opened cryosparc_P3_J50_002_volume_map.mrc as #2, grid size 128,128,128, pixel
3.35, shown at level 0.63, step 1, values float32
Opened cryosparc_P1_J49_001_volume_map.mrc as #3.1, grid size 128,128,128,
pixel 3.32, shown at level 0.261, step 1, values float32
Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #3.2, grid size
128,128,128, pixel 3.32, shown at level 0.656, step 1, values float32
Opened cryosparc_P3_J51_002_volume_map.mrc as #4, grid size 128,128,128, pixel
3.35, shown at level 0.86, step 1, values float32
Opened cryosparc_P3_J51_002_volume_map_sharp.mrc as #5, grid size 128,128,128,
pixel 3.35, shown at level 1, step 1, values float32
Opened cryosparc_P3_J50_002_volume_map_sharp.mrc z flip as #7, grid size
128,128,128, pixel 3.35, shown at level 0.93, step 1, values float32
Opened cryosparc_P3_J50_002_volume_map.mrc z flip as #8, grid size
128,128,128, pixel 3.35, shown at level 1.18, step 1, values float32
Opened cryosparc_P3_J51_002_volume_map.mrc z flip as #9, grid size
128,128,128, pixel 3.35, shown at level 1.21, step 1, values float32
Opened cryosparc_P3_J51_002_volume_map_sharp.mrc z flip as #10, grid size
128,128,128, pixel 3.35, shown at level 1.23, step 1, values float32
Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #13.1, grid size
128,128,128, pixel 3.32, shown at level 0.595, step 1, values float32
Opened cryosparc_P1_J49_001_volume_map.mrc as #13.2, grid size 128,128,128,
pixel 3.32, shown at level 0.532, step 1, values float32
opened ChimeraX session
> show #!12 models
> sequence chain #12/m
Alignment identifier is 12/m
> select #12/m:1
20 atoms, 22 bonds, 1 residue, 1 model selected
> select #12/m
1611 atoms, 1799 bonds, 76 residues, 1 model selected
> hide sel target a
> sequence chain #12/B
Alignment identifier is 12/B
> select #12/B:20
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/B
1605 atoms, 1625 bonds, 206 residues, 1 model selected
> hide #!13.1 models
> hide #!13 models
> sequence chain #12/l
Alignment identifier is 12/l
> select #12/l:1-2
42 atoms, 46 bonds, 2 residues, 1 model selected
> select #12/l
131 atoms, 147 bonds, 6 residues, 1 model selected
> hide sel target a
> select #12/n
1624 atoms, 1814 bonds, 75 residues, 1 model selected
> hide sel target a
> select #12/eI
1143 atoms, 1158 bonds, 154 residues, 1 model selected
> hide sel target a
> ~select
Nothing selected
> color #12 #797979ff
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!6 models
> color #6 #ff00004c
> show #!13.1 models
> toolshed show
Downloading bundle ChimeraX_maskChains-1.4-py3-none-any.whl
Installed ChimeraX-maskChains (1.4)
> hide #!13.1 models
> show #!13.1 models
> hide #!13.1 models
> hide #!13 models
> hide #!12 models
> show #!12 models
> show #!13.1 models
> hide #!12 models
> hide #!6 models
> hide #!13 models
> show #!7 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!7 models
> show #!1 models
> volume #1 level 0.339
> volume #10 level 0.3476
> surface dust #1 size 33.5
> surface dust #10 size 33.5
> Vol resample #10 on grid #1
Unknown command: Vol resample #10 on grid #1
> Vol resample #10 ongrid #1
Unknown command: Vol resample #10 ongrid #1
> volume resample #10 onGrid #1
Opened cryosparc_P3_J51_002_volume_map_sharp.mrc z flip resampled as #14, grid
size 128,128,128, pixel 3.35, shown at step 1, values float32
> volume morph #1,10
Map positions are not the same, cryosparc_P3_J51_002_volume_map_sharp.mrc z
flip #10 and cryosparc_P3_J50_002_volume_map_sharp.mrc #1. Use the "volume
resample" command to make a copy of one map with the same grid as the other
map.
> volume resample #10 onGrid #1
Opened cryosparc_P3_J51_002_volume_map_sharp.mrc z flip resampled as #15, grid
size 128,128,128, pixel 3.35, shown at step 1, values float32
> volume resample #1 onGrid #10
Opened cryosparc_P3_J50_002_volume_map_sharp.mrc resampled as #16, grid size
128,128,128, pixel 3.35, shown at step 1, values float32
> hide #!15 target m
> close #15
> volume morph #14,16
Map positions are not the same, cryosparc_P3_J50_002_volume_map_sharp.mrc
resampled #16 and cryosparc_P3_J51_002_volume_map_sharp.mrc z flip resampled
#14. Use the "volume resample" command to make a copy of one map with the same
grid as the other map.
> volume morph #1,14
Opened morph as #15, grid size 128,128,128, pixel 3.35, shown at step 1,
values float32
> volume #14 level 0.339
> hide #!16 target m
> hide #!15 target m
> close #15
> close #16
> volume morph #1,14
Opened morph as #15, grid size 128,128,128, pixel 3.35, shown at step 1,
values float32
> open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2c.map" "/Users/haandrew/Documents/progress/2026/Cryo-
> EM/2025-09-25/PDB 10.1038/S2d.map"
> "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2e.map" "/Users/haandrew/Documents/progress/2026/Cryo-
> EM/2025-09-25/PDB 10.1038/S2f.map"
> "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2b.map" "/Users/haandrew/Documents/progress/2026/Cryo-
> EM/2025-09-25/PDB 10.1038/s2a.map"
Opened S2c.map as #16.1, grid size 400,400,400, pixel 1.32, shown at level
0.295, step 2, values float32
Opened S2d.map as #16.2, grid size 400,400,400, pixel 1.32, shown at level
0.306, step 2, values float32
Opened S2e.map as #16.3, grid size 400,400,400, pixel 1.32, shown at level
0.226, step 2, values float32
Opened S2f.map as #16.4, grid size 400,400,400, pixel 1.32, shown at level
0.188, step 2, values float32
Opened S2b.map as #16.5, grid size 400,400,400, pixel 1.32, shown at level
0.335, step 2, values float32
Opened s2a.map as #16.6, grid size 400,400,400, pixel 1.32, shown at level
0.281, step 2, values float32
> hide #!15 models
> surface dust #16.1 size 13.2
> surface dust #16.2 size 13.2
> surface dust #16.3 size 13.2
> surface dust #16.4 size 13.2
> surface dust #16.5 size 13.2
> surface dust #16.6 size 13.2
> volume #16.6 level 0.3844
> volume #16.5 level 0.6909
> volume #16.4 level 0.2621
> volume #16.3 level 0.3078
> volume #16.2 level 0.5189
> volume #16.1 level 0.5872
> volume #15 level 1.1
> volume #14 level 1.387
> hide #!14 models
> hide #!15 models
> select add #16
13 models selected
> select subtract #16.1
11 models selected
> select add #16
13 models selected
> show #!1 models
> ui mousemode right "translate selected models"
> volume #1 level 1.765
> volume #1 level 1
> view matrix models #16,1,0,0,-678.03,0,1,0,-283.98,0,0,1,339.69
> view matrix models #16,1,0,0,-665.75,0,1,0,-16.701,0,0,1,289.98
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.5719,-0.81933,-0.040274,45.663,0.56554,-0.42937,0.70413,57.098,-0.59421,0.37992,0.70893,426.98
> view matrix models
> #16,-0.27195,-0.61105,0.74341,-308.36,0.96178,-0.1468,0.23117,-18.477,-0.032125,0.77786,0.62761,166.42
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.27195,-0.61105,0.74341,-283.91,0.96178,-0.1468,0.23117,93.066,-0.032125,0.77786,0.62761,417.76
> view matrix models
> #16,-0.27195,-0.61105,0.74341,-629.81,0.96178,-0.1468,0.23117,251.14,-0.032125,0.77786,0.62761,415.87
> view matrix models
> #16,-0.27195,-0.61105,0.74341,-465.06,0.96178,-0.1468,0.23117,-175.25,-0.032125,0.77786,0.62761,583.7
> view matrix models
> #16,-0.27195,-0.61105,0.74341,-253.52,0.96178,-0.1468,0.23117,-205.13,-0.032125,0.77786,0.62761,488.12
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.30075,-0.67254,0.6762,-209.33,0.82764,-0.53635,-0.16534,53.061,0.47388,0.50992,0.71793,396.32
> view matrix models
> #16,-0.30115,-0.67288,0.67568,-208.97,0.82551,-0.53865,-0.1685,55.208,0.47733,0.50703,0.71768,396.25
> view matrix models
> #16,-0.29833,-0.67034,0.67945,-211.54,0.84053,-0.5218,-0.14574,39.889,0.45223,0.52762,0.7191,397.11
> view matrix models
> #16,-0.29733,-0.66938,0.68082,-212.47,0.84577,-0.51552,-0.13749,34.344,0.44301,0.53494,0.71943,397.55
> view matrix models
> #16,-0.29941,-0.67134,0.67798,-210.54,0.83479,-0.52842,-0.15458,45.837,0.46203,0.51969,0.71864,396.73
> view matrix models
> #16,-0.56519,-0.48619,0.66647,-184.83,-0.80838,0.48755,-0.32986,270.1,-0.16456,-0.7252,-0.66859,1310.6
> view matrix models
> #16,-0.56951,-0.52622,0.63146,-162.55,-0.81193,0.24036,-0.53198,397.23,0.12816,-0.81567,-0.56414,1224.7
> view matrix models
> #16,0.55442,-0.30186,-0.77557,-188.91,-0.16336,-0.95325,0.25423,355.51,-0.81605,-0.014253,-0.57781,1266.7
> view matrix models
> #16,0.24478,0.4158,0.8759,-742.76,0.33051,-0.88506,0.32778,172.1,0.91151,0.20926,-0.35407,638.27
> view matrix models
> #16,-0.36943,-0.91976,0.13252,25.661,0.66521,-0.36133,-0.65341,176.29,0.64886,-0.15323,0.74532,534.48
> view matrix models
> #16,-0.078622,-0.92521,0.37121,-120.35,0.98665,-0.12549,-0.10381,-131.17,0.14263,0.35809,0.92273,484.42
> view matrix models
> #16,0.14538,-0.9787,0.14496,-111.03,0.53355,-0.045831,-0.84453,171.31,0.83318,0.20012,0.51552,436.19
> view matrix models
> #16,-0.59757,-0.47398,0.64673,-174.97,0.79931,-0.41586,0.43377,-130.99,0.063352,0.77615,0.62736,461
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.59757,-0.47398,0.64673,-162.92,0.79931,-0.41586,0.43377,162.56,0.063352,0.77615,0.62736,392.97
> fitmap #16.1 inMap #1
Fit map S2c.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 26877
points
correlation = 0.5341, correlation about mean = 0.05192, overlap = 1.114e+04
steps = 132, shift = 10.6, angle = 10.8 degrees
Position of S2c.map (#16.1) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99810893 0.02343263 0.05682852 393.64453221
-0.02653555 -0.66966662 0.74218763 -13.40747242
0.05544757 -0.74229207 -0.66777844 1149.28256877
Axis -0.99943354 0.00092973 -0.03364133
Axis point 0.00000000 245.98730135 570.91025330
Rotation angle (degrees) 132.04145146
Shift along axis -432.09741016
> fitmap #16.2-16.6 inMap #1
No atoms or maps for #16.2-16.6
> fitmap #16.2 inMap #1
Fit map S2d.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 34291
points
correlation = 0.5249, correlation about mean = 0.05768, overlap = 1.285e+04
steps = 80, shift = 7.88, angle = 9.15 degrees
Position of S2d.map (#16.2) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99732265 0.01469877 0.07163436 391.65963780
-0.04116480 -0.69679380 0.71608928 1.94445090
0.06044001 -0.71712087 -0.69432317 1147.77959402
Axis -0.99921079 0.00780452 -0.03894717
Axis point 0.00000000 241.64873161 565.12583494
Rotation angle (degrees) 134.17858995
Shift along axis -436.03812468
> fitmap #16.3 inMap #1
Fit map S2e.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 42823
points
correlation = 0.5058, correlation about mean = 0.02565, overlap = 8112
steps = 112, shift = 6.98, angle = 6.94 degrees
Position of S2e.map (#16.3) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.98397250 0.05446366 0.16979935 361.02512654
-0.07687108 -0.72964112 0.67949589 25.32942925
0.16090042 -0.68165794 -0.71376012 1119.44431731
Axis -0.99535623 0.00650742 -0.09603974
Axis point 0.00000000 227.23380549 536.67215222
Rotation angle (degrees) 136.86245385
Shift along axis -466.69491855
> fitmap #16.4 inMap #1
Fit map S2f.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 43363
points
correlation = 0.5083, correlation about mean = 0.0391, overlap = 7379
steps = 104, shift = 7, angle = 7.68 degrees
Position of S2f.map (#16.4) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.98309592 0.04540673 0.17737145 361.73202821
-0.08952496 -0.72583984 0.68201305 27.98663913
0.15971125 -0.68636342 -0.70950516 1119.27620975
Axis -0.99509141 0.01284260 -0.09812312
Axis point 0.00000000 231.12753057 534.99539559
Rotation angle (degrees) 136.56247695
Shift along axis -469.42389111
> fitmap #16.5 inMap #1
Fit map S2b.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 25782
points
correlation = 0.5326, correlation about mean = 0.04093, overlap = 1.336e+04
steps = 92, shift = 11.3, angle = 11.6 degrees
Position of S2b.map (#16.5) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99758587 0.01719536 0.06728118 392.17788535
-0.03933875 -0.65847861 0.75157061 -14.75909954
0.05722675 -0.75240297 -0.65621252 1147.82367441
Axis -0.99927195 0.00668038 -0.03756246
Axis point 0.00000000 250.81144779 569.23174617
Rotation angle (degrees) 131.18958139
Shift along axis -435.10603847
> fitmap #16.6 inMap #1
Fit map s2a.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 50384
points
correlation = 0.502, correlation about mean = 0.05148, overlap = 1.342e+04
steps = 120, shift = 8.31, angle = 8.12 degrees
Position of s2a.map (#16.6) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.98166052 0.02721070 0.18868544 363.50315852
-0.10799927 -0.73623369 0.66805397 41.35862859
0.15709479 -0.67618010 -0.71979281 1120.96045999
Axis -0.99470748 0.02337647 -0.10005279
Axis point 0.00000000 234.86628620 531.95176394
Rotation angle (degrees) 137.49199920
Shift along axis -472.76771662
> view matrix models
> #16,-0.59757,-0.47398,0.64673,-150.28,0.79931,-0.41586,0.43377,-63.822,0.063352,0.77615,0.62736,633.15
> view matrix models
> #16,-0.59757,-0.47398,0.64673,-170.34,0.79931,-0.41586,0.43377,-30.907,0.063352,0.77615,0.62736,560.41
> view matrix models
> #16,-0.59757,-0.47398,0.64673,-174.48,0.79931,-0.41586,0.43377,206.88,0.063352,0.77615,0.62736,454.83
> view matrix models
> #16,-0.59757,-0.47398,0.64673,-130.36,0.79931,-0.41586,0.43377,173.27,0.063352,0.77615,0.62736,397.21
> view matrix models
> #16,-0.59757,-0.47398,0.64673,-260.11,0.79931,-0.41586,0.43377,-158.3,0.063352,0.77615,0.62736,510.19
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.26639,-0.56479,-0.78106,-109.82,0.082779,-0.79394,0.60234,115.71,-0.9603,-0.22511,-0.16475,1307.6
> view matrix models
> #16,0.53583,0.33757,-0.77391,-453.36,0.10734,-0.9364,-0.33412,393.78,-0.83748,0.095965,-0.53798,1275.9
> view matrix models
> #16,0.67058,0.18488,-0.71843,-462.52,0.074315,-0.98032,-0.18291,376.36,-0.73811,0.069263,-0.67112,1289.7
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.67058,0.18488,-0.71843,-396.26,0.074315,-0.98032,-0.18291,713.53,-0.73811,0.069263,-0.67112,1160.8
> view matrix models
> #16,0.67058,0.18488,-0.71843,-317.89,0.074315,-0.98032,-0.18291,710.12,-0.73811,0.069263,-0.67112,1168.8
> fitmap #16.6 inMap #1
Fit map s2a.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 50384
points
correlation = 0.8927, correlation about mean = 0.3357, overlap = 4.1e+04
steps = 92, shift = 16.1, angle = 5.12 degrees
Position of s2a.map (#16.6) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99203477 0.01414933 0.12516715 381.41899028
-0.06819224 -0.77514308 0.62809475 38.12321307
0.10590957 -0.63162726 -0.76800401 1128.06691755
Axis -0.99775445 0.01525284 -0.06521809
Axis point 0.00000000 217.69374214 543.54280324
Rotation angle (degrees) 140.85548372
Shift along axis -453.55138409
> fitmap #16.5 inMap #1
Fit map S2b.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 25782
points
correlation = 0.902, correlation about mean = 0.1696, overlap = 3.938e+04
steps = 88, shift = 20.1, angle = 9.86 degrees
Position of S2b.map (#16.5) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99274117 0.01281206 0.11958600 382.94969972
-0.06603953 -0.77293742 0.63103607 36.40729845
0.10051736 -0.63435290 -0.76648070 1129.64421589
Axis -0.99795125 0.01503851 -0.06218644
Axis point 0.00000000 218.40206678 545.15188456
Rotation angle (degrees) 140.65463473
Shift along axis -451.86617282
> fitmap #16.4 inMap #1
Fit map S2f.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 43363
points
correlation = 0.9339, correlation about mean = 0.3669, overlap = 2.56e+04
steps = 72, shift = 13.6, angle = 5.57 degrees
Position of S2f.map (#16.4) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99236513 0.01304928 0.12264244 382.22103763
-0.06769560 -0.77358126 0.63007090 37.15149401
0.10309586 -0.63356275 -0.76679169 1128.88862407
Axis -0.99784580 0.01543522 -0.06376131
Axis point 0.00000000 218.26587127 544.33816557
Rotation angle (degrees) 140.71481055
Shift along axis -452.80363621
> fitmap #16.3 inMap #1
Fit map S2e.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 42823
points
correlation = 0.9317, correlation about mean = 0.4405, overlap = 2.82e+04
steps = 84, shift = 13, angle = 5.3 degrees
Position of S2e.map (#16.3) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99234096 0.01417734 0.12271276 381.96111981
-0.06673881 -0.77440109 0.62916523 37.29862155
0.10394879 -0.63253613 -0.76752374 1128.60860135
Axis -0.99783994 0.01483984 -0.06399404
Axis point 0.00000000 217.76891440 544.19917409
Rotation angle (degrees) 140.78617247
Shift along axis -452.80677789
> fitmap #16.2 inMap #1
Fit map S2d.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 34291
points
correlation = 0.9094, correlation about mean = 0.2285, overlap = 3.997e+04
steps = 80, shift = 16.8, angle = 6.96 degrees
Position of S2d.map (#16.2) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99275819 0.01276894 0.11944928 383.01504979
-0.06602558 -0.77268558 0.63134587 36.23777294
0.10035835 -0.63466049 -0.76624687 1129.66166308
Axis -0.99795576 0.01504882 -0.06211141
Axis point 0.00000000 218.45159371 545.19781059
Rotation angle (degrees) 140.63192584
Shift along axis -451.85162120
> fitmap #16.1 inMap #1
Fit map S2c.map in map cryosparc_P3_J50_002_volume_map_sharp.mrc using 26877
points
correlation = 0.912, correlation about mean = 0.2011, overlap = 3.432e+04
steps = 68, shift = 19.4, angle = 9.17 degrees
Position of S2c.map (#16.1) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99281982 0.01183988 0.11903198 383.32880232
-0.06657916 -0.77201081 0.63211274 35.96713020
0.09937811 -0.63549911 -0.76567935 1129.95128091
Axis -0.99797243 0.01547320 -0.06173818
Axis point 0.00000000 218.79992284 545.40679752
Rotation angle (degrees) 140.57307169
Shift along axis -451.75618232
> hide #!16 models
> show #!16 models
> select subtract #16
Nothing selected
> open /Users/haandrew/Downloads/cryosparc_P1_J125_001_volume_map_sharp.mrc
Opened cryosparc_P1_J125_001_volume_map_sharp.mrc as #17, grid size
128,128,128, pixel 3.32, shown at level 1.1, step 1, values float32
> open /Users/haandrew/Downloads/cryosparc_P1_J125_001_volume_map.mrc
Opened cryosparc_P1_J125_001_volume_map.mrc as #18, grid size 128,128,128,
pixel 3.32, shown at level 0.954, step 1, values float32
> open /Users/haandrew/Downloads/cryosparc_P1_J124_001_volume_map_sharp.mrc
Opened cryosparc_P1_J124_001_volume_map_sharp.mrc as #19, grid size
128,128,128, pixel 3.32, shown at level 1.13, step 1, values float32
> open /Users/haandrew/Downloads/cryosparc_P1_J124_001_volume_map.mrc
Opened cryosparc_P1_J124_001_volume_map.mrc as #20, grid size 128,128,128,
pixel 3.32, shown at level 0.953, step 1, values float32
> open /Users/haandrew/Downloads/cryosparc_P1_J123_001_volume_map_sharp.mrc
Opened cryosparc_P1_J123_001_volume_map_sharp.mrc as #21, grid size
128,128,128, pixel 3.32, shown at level 0.958, step 1, values float32
> open /Users/haandrew/Downloads/cryosparc_P1_J123_001_volume_map.mrc
Opened cryosparc_P1_J123_001_volume_map.mrc as #22, grid size 128,128,128,
pixel 3.32, shown at level 0.868, step 1, values float32
> open /Users/haandrew/Downloads/cryosparc_P1_J122_002_volume_map_sharp.mrc
Opened cryosparc_P1_J122_002_volume_map_sharp.mrc as #23, grid size
128,128,128, pixel 3.32, shown at level 1.03, step 1, values float32
> open /Users/haandrew/Downloads/cryosparc_P1_J122_002_volume_map.mrc
Opened cryosparc_P1_J122_002_volume_map.mrc as #24, grid size 128,128,128,
pixel 3.32, shown at level 0.916, step 1, values float32
> open /Users/haandrew/Downloads/cryosparc_P1_J121_001_volume_map.mrc
Opened cryosparc_P1_J121_001_volume_map.mrc as #25, grid size 128,128,128,
pixel 3.32, shown at level 0.97, step 1, values float32
> open /Users/haandrew/Downloads/cryosparc_P1_J121_001_volume_map_sharp.mrc
Opened cryosparc_P1_J121_001_volume_map_sharp.mrc as #26, grid size
128,128,128, pixel 3.32, shown at level 1.13, step 1, values float32
> hide #!16.6 models
> hide #!16.5 models
> hide #!16.4 models
> hide #!16.3 models
> hide #!16.2 models
> hide #!16.1 models
> hide #!16 models
> select add #17
2 models selected
> select add #18
4 models selected
> select add #19
6 models selected
> select add #20
8 models selected
> select add #21
10 models selected
> select add #22
12 models selected
> select add #23
14 models selected
> select add #24
16 models selected
> select add #25
18 models selected
> select add #26
20 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.99574,-0.089546,-0.022173,24.724,0.074812,0.92447,-0.37385,77.669,0.053976,0.3706,0.92722,-76,#18,0.99574,-0.089546,-0.022173,24.724,0.074812,0.92447,-0.37385,77.669,0.053976,0.3706,0.92722,-76,#19,0.99574,-0.089546,-0.022173,24.724,0.074812,0.92447,-0.37385,77.669,0.053976,0.3706,0.92722,-76,#20,0.99574,-0.089546,-0.022173,24.724,0.074812,0.92447,-0.37385,77.669,0.053976,0.3706,0.92722,-76,#21,0.99574,-0.089546,-0.022173,24.724,0.074812,0.92447,-0.37385,77.669,0.053976,0.3706,0.92722,-76,#22,0.99574,-0.089546,-0.022173,24.724,0.074812,0.92447,-0.37385,77.669,0.053976,0.3706,0.92722,-76,#23,0.99574,-0.089546,-0.022173,24.724,0.074812,0.92447,-0.37385,77.669,0.053976,0.3706,0.92722,-76,#24,0.99574,-0.089546,-0.022173,24.724,0.074812,0.92447,-0.37385,77.669,0.053976,0.3706,0.92722,-76,#25,0.99574,-0.089546,-0.022173,24.724,0.074812,0.92447,-0.37385,77.669,0.053976,0.3706,0.92722,-76,#26,0.99574,-0.089546,-0.022173,24.724,0.074812,0.92447,-0.37385,77.669,0.053976,0.3706,0.92722,-76
> view matrix models
> #17,0.98267,-0.18522,-0.0073187,44.806,0.12534,0.69302,-0.70994,186.22,0.13656,0.69672,0.70423,-116.67,#18,0.98267,-0.18522,-0.0073187,44.806,0.12534,0.69302,-0.70994,186.22,0.13656,0.69672,0.70423,-116.67,#19,0.98267,-0.18522,-0.0073187,44.806,0.12534,0.69302,-0.70994,186.22,0.13656,0.69672,0.70423,-116.67,#20,0.98267,-0.18522,-0.0073187,44.806,0.12534,0.69302,-0.70994,186.22,0.13656,0.69672,0.70423,-116.67,#21,0.98267,-0.18522,-0.0073187,44.806,0.12534,0.69302,-0.70994,186.22,0.13656,0.69672,0.70423,-116.67,#22,0.98267,-0.18522,-0.0073187,44.806,0.12534,0.69302,-0.70994,186.22,0.13656,0.69672,0.70423,-116.67,#23,0.98267,-0.18522,-0.0073187,44.806,0.12534,0.69302,-0.70994,186.22,0.13656,0.69672,0.70423,-116.67,#24,0.98267,-0.18522,-0.0073187,44.806,0.12534,0.69302,-0.70994,186.22,0.13656,0.69672,0.70423,-116.67,#25,0.98267,-0.18522,-0.0073187,44.806,0.12534,0.69302,-0.70994,186.22,0.13656,0.69672,0.70423,-116.67,#26,0.98267,-0.18522,-0.0073187,44.806,0.12534,0.69302,-0.70994,186.22,0.13656,0.69672,0.70423,-116.67
> view matrix models
> #17,0.99981,-0.018101,-0.0075164,5.3917,0.017437,0.9966,-0.080558,13.215,0.008949,0.080412,0.99672,-18.299,#18,0.99981,-0.018101,-0.0075164,5.3917,0.017437,0.9966,-0.080558,13.215,0.008949,0.080412,0.99672,-18.299,#19,0.99981,-0.018101,-0.0075164,5.3917,0.017437,0.9966,-0.080558,13.215,0.008949,0.080412,0.99672,-18.299,#20,0.99981,-0.018101,-0.0075164,5.3917,0.017437,0.9966,-0.080558,13.215,0.008949,0.080412,0.99672,-18.299,#21,0.99981,-0.018101,-0.0075164,5.3917,0.017437,0.9966,-0.080558,13.215,0.008949,0.080412,0.99672,-18.299,#22,0.99981,-0.018101,-0.0075164,5.3917,0.017437,0.9966,-0.080558,13.215,0.008949,0.080412,0.99672,-18.299,#23,0.99981,-0.018101,-0.0075164,5.3917,0.017437,0.9966,-0.080558,13.215,0.008949,0.080412,0.99672,-18.299,#24,0.99981,-0.018101,-0.0075164,5.3917,0.017437,0.9966,-0.080558,13.215,0.008949,0.080412,0.99672,-18.299,#25,0.99981,-0.018101,-0.0075164,5.3917,0.017437,0.9966,-0.080558,13.215,0.008949,0.080412,0.99672,-18.299,#26,0.99981,-0.018101,-0.0075164,5.3917,0.017437,0.9966,-0.080558,13.215,0.008949,0.080412,0.99672,-18.299
> view matrix models
> #17,0.99764,-0.065718,-0.019769,18.608,0.057572,0.95824,-0.28012,54.266,0.037353,0.27832,0.95976,-59.143,#18,0.99764,-0.065718,-0.019769,18.608,0.057572,0.95824,-0.28012,54.266,0.037353,0.27832,0.95976,-59.143,#19,0.99764,-0.065718,-0.019769,18.608,0.057572,0.95824,-0.28012,54.266,0.037353,0.27832,0.95976,-59.143,#20,0.99764,-0.065718,-0.019769,18.608,0.057572,0.95824,-0.28012,54.266,0.037353,0.27832,0.95976,-59.143,#21,0.99764,-0.065718,-0.019769,18.608,0.057572,0.95824,-0.28012,54.266,0.037353,0.27832,0.95976,-59.143,#22,0.99764,-0.065718,-0.019769,18.608,0.057572,0.95824,-0.28012,54.266,0.037353,0.27832,0.95976,-59.143,#23,0.99764,-0.065718,-0.019769,18.608,0.057572,0.95824,-0.28012,54.266,0.037353,0.27832,0.95976,-59.143,#24,0.99764,-0.065718,-0.019769,18.608,0.057572,0.95824,-0.28012,54.266,0.037353,0.27832,0.95976,-59.143,#25,0.99764,-0.065718,-0.019769,18.608,0.057572,0.95824,-0.28012,54.266,0.037353,0.27832,0.95976,-59.143,#26,0.99764,-0.065718,-0.019769,18.608,0.057572,0.95824,-0.28012,54.266,0.037353,0.27832,0.95976,-59.143
> view matrix models
> #17,1,-0.00095368,-0.00043935,0.20138,0.00095177,0.99999,-0.0043156,0.19394,0.00044346,0.0043151,0.99999,-0.82227,#18,1,-0.00095368,-0.00043935,0.20138,0.00095177,0.99999,-0.0043156,0.19394,0.00044346,0.0043151,0.99999,-0.82227,#19,1,-0.00095368,-0.00043935,0.20138,0.00095177,0.99999,-0.0043156,0.19394,0.00044346,0.0043151,0.99999,-0.82227,#20,1,-0.00095368,-0.00043935,0.20138,0.00095177,0.99999,-0.0043156,0.19394,0.00044346,0.0043151,0.99999,-0.82227,#21,1,-0.00095368,-0.00043935,0.20138,0.00095177,0.99999,-0.0043156,0.19394,0.00044346,0.0043151,0.99999,-0.82227,#22,1,-0.00095368,-0.00043935,0.20138,0.00095177,0.99999,-0.0043156,0.19394,0.00044346,0.0043151,0.99999,-0.82227,#23,1,-0.00095368,-0.00043935,0.20138,0.00095177,0.99999,-0.0043156,0.19394,0.00044346,0.0043151,0.99999,-0.82227,#24,1,-0.00095368,-0.00043935,0.20138,0.00095177,0.99999,-0.0043156,0.19394,0.00044346,0.0043151,0.99999,-0.82227,#25,1,-0.00095368,-0.00043935,0.20138,0.00095177,0.99999,-0.0043156,0.19394,0.00044346,0.0043151,0.99999,-0.82227,#26,1,-0.00095368,-0.00043935,0.20138,0.00095177,0.99999,-0.0043156,0.19394,0.00044346,0.0043151,0.99999,-0.82227
> ui mousemode right "translate selected models"
> view matrix models
> #17,1,-0.00095368,-0.00043935,-64.716,0.00095177,0.99999,-0.0043156,341.09,0.00044346,0.0043151,0.99999,451.16,#18,1,-0.00095368,-0.00043935,-64.716,0.00095177,0.99999,-0.0043156,341.09,0.00044346,0.0043151,0.99999,451.16,#19,1,-0.00095368,-0.00043935,-64.716,0.00095177,0.99999,-0.0043156,341.09,0.00044346,0.0043151,0.99999,451.16,#20,1,-0.00095368,-0.00043935,-64.716,0.00095177,0.99999,-0.0043156,341.09,0.00044346,0.0043151,0.99999,451.16,#21,1,-0.00095368,-0.00043935,-64.716,0.00095177,0.99999,-0.0043156,341.09,0.00044346,0.0043151,0.99999,451.16,#22,1,-0.00095368,-0.00043935,-64.716,0.00095177,0.99999,-0.0043156,341.09,0.00044346,0.0043151,0.99999,451.16,#23,1,-0.00095368,-0.00043935,-64.716,0.00095177,0.99999,-0.0043156,341.09,0.00044346,0.0043151,0.99999,451.16,#24,1,-0.00095368,-0.00043935,-64.716,0.00095177,0.99999,-0.0043156,341.09,0.00044346,0.0043151,0.99999,451.16,#25,1,-0.00095368,-0.00043935,-64.716,0.00095177,0.99999,-0.0043156,341.09,0.00044346,0.0043151,0.99999,451.16,#26,1,-0.00095368,-0.00043935,-64.716,0.00095177,0.99999,-0.0043156,341.09,0.00044346,0.0043151,0.99999,451.16
> view matrix models
> #17,1,-0.00095368,-0.00043935,-365.11,0.00095177,0.99999,-0.0043156,367.08,0.00044346,0.0043151,0.99999,319.04,#18,1,-0.00095368,-0.00043935,-365.11,0.00095177,0.99999,-0.0043156,367.08,0.00044346,0.0043151,0.99999,319.04,#19,1,-0.00095368,-0.00043935,-365.11,0.00095177,0.99999,-0.0043156,367.08,0.00044346,0.0043151,0.99999,319.04,#20,1,-0.00095368,-0.00043935,-365.11,0.00095177,0.99999,-0.0043156,367.08,0.00044346,0.0043151,0.99999,319.04,#21,1,-0.00095368,-0.00043935,-365.11,0.00095177,0.99999,-0.0043156,367.08,0.00044346,0.0043151,0.99999,319.04,#22,1,-0.00095368,-0.00043935,-365.11,0.00095177,0.99999,-0.0043156,367.08,0.00044346,0.0043151,0.99999,319.04,#23,1,-0.00095368,-0.00043935,-365.11,0.00095177,0.99999,-0.0043156,367.08,0.00044346,0.0043151,0.99999,319.04,#24,1,-0.00095368,-0.00043935,-365.11,0.00095177,0.99999,-0.0043156,367.08,0.00044346,0.0043151,0.99999,319.04,#25,1,-0.00095368,-0.00043935,-365.11,0.00095177,0.99999,-0.0043156,367.08,0.00044346,0.0043151,0.99999,319.04,#26,1,-0.00095368,-0.00043935,-365.11,0.00095177,0.99999,-0.0043156,367.08,0.00044346,0.0043151,0.99999,319.04
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.48948,0.47528,-0.73111,3.4981,-0.87199,-0.26059,0.41439,735.43,0.0064326,0.84035,0.542,234.87,#18,-0.48948,0.47528,-0.73111,3.4981,-0.87199,-0.26059,0.41439,735.43,0.0064326,0.84035,0.542,234.87,#19,-0.48948,0.47528,-0.73111,3.4981,-0.87199,-0.26059,0.41439,735.43,0.0064326,0.84035,0.542,234.87,#20,-0.48948,0.47528,-0.73111,3.4981,-0.87199,-0.26059,0.41439,735.43,0.0064326,0.84035,0.542,234.87,#21,-0.48948,0.47528,-0.73111,3.4981,-0.87199,-0.26059,0.41439,735.43,0.0064326,0.84035,0.542,234.87,#22,-0.48948,0.47528,-0.73111,3.4981,-0.87199,-0.26059,0.41439,735.43,0.0064326,0.84035,0.542,234.87,#23,-0.48948,0.47528,-0.73111,3.4981,-0.87199,-0.26059,0.41439,735.43,0.0064326,0.84035,0.542,234.87,#24,-0.48948,0.47528,-0.73111,3.4981,-0.87199,-0.26059,0.41439,735.43,0.0064326,0.84035,0.542,234.87,#25,-0.48948,0.47528,-0.73111,3.4981,-0.87199,-0.26059,0.41439,735.43,0.0064326,0.84035,0.542,234.87,#26,-0.48948,0.47528,-0.73111,3.4981,-0.87199,-0.26059,0.41439,735.43,0.0064326,0.84035,0.542,234.87
> view matrix models
> #17,-0.97283,-0.0066229,-0.23144,105.34,-0.15909,-0.70715,0.68893,621.22,-0.16823,0.70703,0.68688,270.55,#18,-0.97283,-0.0066229,-0.23144,105.34,-0.15909,-0.70715,0.68893,621.22,-0.16823,0.70703,0.68688,270.55,#19,-0.97283,-0.0066229,-0.23144,105.34,-0.15909,-0.70715,0.68893,621.22,-0.16823,0.70703,0.68688,270.55,#20,-0.97283,-0.0066229,-0.23144,105.34,-0.15909,-0.70715,0.68893,621.22,-0.16823,0.70703,0.68688,270.55,#21,-0.97283,-0.0066229,-0.23144,105.34,-0.15909,-0.70715,0.68893,621.22,-0.16823,0.70703,0.68688,270.55,#22,-0.97283,-0.0066229,-0.23144,105.34,-0.15909,-0.70715,0.68893,621.22,-0.16823,0.70703,0.68688,270.55,#23,-0.97283,-0.0066229,-0.23144,105.34,-0.15909,-0.70715,0.68893,621.22,-0.16823,0.70703,0.68688,270.55,#24,-0.97283,-0.0066229,-0.23144,105.34,-0.15909,-0.70715,0.68893,621.22,-0.16823,0.70703,0.68688,270.55,#25,-0.97283,-0.0066229,-0.23144,105.34,-0.15909,-0.70715,0.68893,621.22,-0.16823,0.70703,0.68688,270.55,#26,-0.97283,-0.0066229,-0.23144,105.34,-0.15909,-0.70715,0.68893,621.22,-0.16823,0.70703,0.68688,270.55
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.97283,-0.0066229,-0.23144,36.511,-0.15909,-0.70715,0.68893,429.96,-0.16823,0.70703,0.68688,544.99,#18,-0.97283,-0.0066229,-0.23144,36.511,-0.15909,-0.70715,0.68893,429.96,-0.16823,0.70703,0.68688,544.99,#19,-0.97283,-0.0066229,-0.23144,36.511,-0.15909,-0.70715,0.68893,429.96,-0.16823,0.70703,0.68688,544.99,#20,-0.97283,-0.0066229,-0.23144,36.511,-0.15909,-0.70715,0.68893,429.96,-0.16823,0.70703,0.68688,544.99,#21,-0.97283,-0.0066229,-0.23144,36.511,-0.15909,-0.70715,0.68893,429.96,-0.16823,0.70703,0.68688,544.99,#22,-0.97283,-0.0066229,-0.23144,36.511,-0.15909,-0.70715,0.68893,429.96,-0.16823,0.70703,0.68688,544.99,#23,-0.97283,-0.0066229,-0.23144,36.511,-0.15909,-0.70715,0.68893,429.96,-0.16823,0.70703,0.68688,544.99,#24,-0.97283,-0.0066229,-0.23144,36.511,-0.15909,-0.70715,0.68893,429.96,-0.16823,0.70703,0.68688,544.99,#25,-0.97283,-0.0066229,-0.23144,36.511,-0.15909,-0.70715,0.68893,429.96,-0.16823,0.70703,0.68688,544.99,#26,-0.97283,-0.0066229,-0.23144,36.511,-0.15909,-0.70715,0.68893,429.96,-0.16823,0.70703,0.68688,544.99
> view matrix models
> #17,-0.97283,-0.0066229,-0.23144,-9.3426,-0.15909,-0.70715,0.68893,441.91,-0.16823,0.70703,0.68688,533.22,#18,-0.97283,-0.0066229,-0.23144,-9.3426,-0.15909,-0.70715,0.68893,441.91,-0.16823,0.70703,0.68688,533.22,#19,-0.97283,-0.0066229,-0.23144,-9.3426,-0.15909,-0.70715,0.68893,441.91,-0.16823,0.70703,0.68688,533.22,#20,-0.97283,-0.0066229,-0.23144,-9.3426,-0.15909,-0.70715,0.68893,441.91,-0.16823,0.70703,0.68688,533.22,#21,-0.97283,-0.0066229,-0.23144,-9.3426,-0.15909,-0.70715,0.68893,441.91,-0.16823,0.70703,0.68688,533.22,#22,-0.97283,-0.0066229,-0.23144,-9.3426,-0.15909,-0.70715,0.68893,441.91,-0.16823,0.70703,0.68688,533.22,#23,-0.97283,-0.0066229,-0.23144,-9.3426,-0.15909,-0.70715,0.68893,441.91,-0.16823,0.70703,0.68688,533.22,#24,-0.97283,-0.0066229,-0.23144,-9.3426,-0.15909,-0.70715,0.68893,441.91,-0.16823,0.70703,0.68688,533.22,#25,-0.97283,-0.0066229,-0.23144,-9.3426,-0.15909,-0.70715,0.68893,441.91,-0.16823,0.70703,0.68688,533.22,#26,-0.97283,-0.0066229,-0.23144,-9.3426,-0.15909,-0.70715,0.68893,441.91,-0.16823,0.70703,0.68688,533.22
> fitmap #17 inMap #1
Fit map cryosparc_P1_J125_001_volume_map_sharp.mrc in map
cryosparc_P3_J50_002_volume_map_sharp.mrc using 20969 points
correlation = 0.9436, correlation about mean = 0.3712, overlap = 4.794e+04
steps = 112, shift = 11.6, angle = 16.9 degrees
Position of cryosparc_P1_J125_001_volume_map_sharp.mrc (#17) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97473724 0.22318025 0.00882537 372.40183303
0.22334198 0.97349942 0.04916529 -54.48498320
0.00238123 0.04989432 -0.99875166 409.83031245
Axis 0.11237811 0.99335273 0.02493025
Axis point 189.61746377 0.00000000 205.29466945
Rotation angle (degrees) 179.81415339
Shift along axis -2.05582236
> fitmap #18 inMap #1
Fit map cryosparc_P1_J125_001_volume_map.mrc in map
cryosparc_P3_J50_002_volume_map_sharp.mrc using 20953 points
correlation = 0.9437, correlation about mean = 0.3519, overlap = 3.992e+04
steps = 112, shift = 11.4, angle = 16.9 degrees
Position of cryosparc_P1_J125_001_volume_map.mrc (#18) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97474890 0.22312942 0.00882287 372.41512470
0.22329174 0.97352491 0.04888804 -54.44207992
0.00231908 0.04962363 -0.99876529 409.85155947
Axis 0.11235195 0.99335914 0.02479219
Axis point 189.62405682 0.00000000 205.29814212
Rotation angle (degrees) 179.81243421
Shift along axis -2.07785457
> fitmap #19 inMap #1
Fit map cryosparc_P1_J124_001_volume_map_sharp.mrc in map
cryosparc_P3_J50_002_volume_map_sharp.mrc using 20960 points
correlation = 0.9446, correlation about mean = 0.3793, overlap = 5.003e+04
steps = 116, shift = 11.8, angle = 16.9 degrees
Position of cryosparc_P1_J124_001_volume_map_sharp.mrc (#19) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97470685 0.22329345 0.00930525 372.32314802
0.22347991 0.97349216 0.04867993 -54.33225066
0.00181133 0.04952820 -0.99877108 410.02364850
Axis 0.11244159 0.99335090 0.02471608
Axis point 189.62591492 0.00000000 205.33409228
Rotation angle (degrees) 179.78387742
Shift along axis -1.97220587
> fitmap #20 inMap #1
Fit map cryosparc_P1_J124_001_volume_map.mrc in map
cryosparc_P3_J50_002_volume_map_sharp.mrc using 20947 points
correlation = 0.9462, correlation about mean = 0.3696, overlap = 4.053e+04
steps = 112, shift = 11.8, angle = 16.9 degrees
Position of cryosparc_P1_J124_001_volume_map.mrc (#20) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97467049 0.22345442 0.00924890 372.30483215
0.22363779 0.97345306 0.04873675 -54.37554808
0.00188707 0.04957068 -0.99876883 409.96318277
Axis 0.11252294 0.99334106 0.02474131
Axis point 189.61455386 0.00000000 205.31133885
Rotation angle (degrees) 179.78768492
Shift along axis -1.97760389
> fitmap #21 inMap #1
Fit map cryosparc_P1_J123_001_volume_map_sharp.mrc in map
cryosparc_P3_J50_002_volume_map_sharp.mrc using 20963 points
correlation = 0.9209, correlation about mean = 0.2851, overlap = 3.745e+04
steps = 100, shift = 11.7, angle = 16.9 degrees
Position of cryosparc_P1_J123_001_volume_map_sharp.mrc (#21) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97475528 0.22307796 0.00940001 372.49506038
0.22326526 0.97343319 0.05079800 -54.72356346
0.00218163 0.05161431 -0.99866470 409.47423623
Axis 0.11233499 0.99333606 0.02577453
Axis point 189.71632473 0.00000000 205.10625789
Rotation angle (degrees) 179.79182095
Shift along axis -1.96065387
> fitmap #22 inMap #1
Fit map cryosparc_P1_J123_001_volume_map.mrc in map
cryosparc_P3_J50_002_volume_map_sharp.mrc using 20968 points
correlation = 0.916, correlation about mean = 0.2616, overlap = 3.287e+04
steps = 92, shift = 11.7, angle = 16.9 degrees
Position of cryosparc_P1_J123_001_volume_map.mrc (#22) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97474433 0.22313996 0.00905743 372.54938107
0.22330958 0.97342454 0.05076901 -54.75965753
0.00251187 0.05150942 -0.99866934 409.39735460
Axis 0.11236195 0.99333388 0.02574084
Axis point 189.71130805 0.00000000 205.09907729
Rotation angle (degrees) 179.81122498
Shift along axis -1.99601695
> fitmap #23 inMap #1
Fit map cryosparc_P1_J122_002_volume_map_sharp.mrc in map
cryosparc_P3_J50_002_volume_map_sharp.mrc using 20963 points
correlation = 0.9267, correlation about mean = 0.2962, overlap = 4.11e+04
steps = 116, shift = 11.7, angle = 16.8 degrees
Position of cryosparc_P1_J122_002_volume_map_sharp.mrc (#23) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97494510 0.22230195 0.00799320 372.70121549
0.22242457 0.97372917 0.04877297 -54.23436251
0.00305911 0.04932885 -0.99877790 409.90832512
Axis 0.11191961 0.99341055 0.02468760
Axis point 189.66189595 0.00000000 205.39499069
Rotation angle (degrees) 179.85771104
Shift along axis -2.04475959
> fitmap #24 inMap #1
Fit map cryosparc_P1_J122_002_volume_map.mrc in map
cryosparc_P3_J50_002_volume_map_sharp.mrc using 20967 points
correlation = 0.9237, correlation about mean = 0.2747, overlap = 3.541e+04
steps = 112, shift = 11.6, angle = 16.8 degrees
Position of cryosparc_P1_J122_002_volume_map.mrc (#24) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97491815 0.22242980 0.00771786 372.71800864
0.22253899 0.97370751 0.04868334 -54.21108610
0.00331369 0.04917980 -0.99878444 409.89485222
Axis 0.11198121 0.99340510 0.02462759
Axis point 189.64315659 0.00000000 205.41135245
Rotation angle (degrees) 179.87299185
Shift along axis -2.02143368
> fitmap #25 inMap #1
Fit map cryosparc_P1_J121_001_volume_map.mrc in map
cryosparc_P3_J50_002_volume_map_sharp.mrc using 20960 points
correlation = 0.9295, correlation about mean = 0.3342, overlap = 3.96e+04
steps = 100, shift = 12.2, angle = 17.2 degrees
Position of cryosparc_P1_J121_001_volume_map.mrc (#25) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97391183 0.22651657 0.01363771 370.37768813
0.22691899 0.97261478 0.05028159 -55.33106904
-0.00187463 0.05206449 -0.99864196 410.22573067
Axis 0.11414490 0.99312999 0.02576373
Axis point 189.17517566 0.00000000 205.10193122
Rotation angle (degrees) 179.55252552
Shift along axis -2.10527514
> fitmap #26 inMap #1
Fit map cryosparc_P1_J121_001_volume_map_sharp.mrc in map
cryosparc_P3_J50_002_volume_map_sharp.mrc using 20966 points
correlation = 0.9273, correlation about mean = 0.3487, overlap = 4.763e+04
steps = 100, shift = 12.2, angle = 17.2 degrees
Position of cryosparc_P1_J121_001_volume_map_sharp.mrc (#26) relative to
cryosparc_P3_J50_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97381510 0.22691539 0.01391205 370.22772018
0.22733192 0.97250985 0.05044581 -55.44775202
-0.00208268 0.05228755 -0.99862989 410.17642890
Axis 0.11435239 0.99310356 0.02586194
Axis point 189.13780372 0.00000000 205.05915510
Rotation angle (degrees) 179.53859786
Shift along axis -2.12097830
> select subtract #17
18 models selected
> select subtract #18
16 models selected
> select subtract #19
14 models selected
> select subtract #20
12 models selected
> select subtract #21
10 models selected
> select subtract #22
8 models selected
> select subtract #23
6 models selected
> select subtract #24
4 models selected
> select subtract #26
2 models selected
> select subtract #25
Nothing selected
> hide #!1 models
> volume #26 level 0.636
> volume #25 level 0.4349
> volume #24 level 0.3978
> surface dust #17 size 33.2
> surface dust #18 size 33.2
> surface dust #19 size 33.2
> surface dust #20 size 33.2
> surface dust #21 size 33.2
> surface dust #22 size 33.2
> surface dust #23 size 33.2
> surface dust #24 size 33.2
> surface dust #25 size 33.2
> surface dust #26 size 33.2
> volume #23 level 0.378
> volume #22 level 0.3412
> volume #21 level 0.3913
> volume #20 level 0.3613
> volume #19 level 0.406
> volume #18 level 0.2841
> volume #17 level 0.6173
> volume #16.6 level 0.2311
> hide #!16.6 models
> hide #!18 models
> hide #!20 models
> hide #!22 models
> hide #!24 models
> hide #!25 models
> show #!18 models
> hide #!17 models
> hide #!19 models
> show #!20 models
> hide #!21 models
> show #!22 models
> hide #!23 models
> show #!24 models
> hide #!26 models
> show #!25 models
> show #!1 models
> hide #!1 models
> volume resample #18 onGrid #25
Opened cryosparc_P1_J125_001_volume_map.mrc resampled as #27, grid size
128,128,128, pixel 3.32, shown at step 1, values float32
> volume resample #20 onGrid #25
Opened cryosparc_P1_J124_001_volume_map.mrc resampled as #28, grid size
128,128,128, pixel 3.32, shown at step 1, values float32
> volume resample #22 onGrid #25
Opened cryosparc_P1_J123_001_volume_map.mrc resampled as #29, grid size
128,128,128, pixel 3.32, shown at step 1, values float32
> volume resample #24 onGrid #25
Opened cryosparc_P1_J122_002_volume_map.mrc resampled as #30, grid size
128,128,128, pixel 3.32, shown at step 1, values float32
> volume morph #25,27-30
Opened morph as #31, grid size 128,128,128, pixel 3.32, shown at step 1,
values float32
> surface dust #31 size 33.2
> show #!16.1 models
> volume #16.6 level 0.1812
> volume #16.5 level 0.1543
> volume #26 color #919191
> volume #27 color #919191
> select add #16.6
3 models selected
> select add #17
5 models selected
> select add #18
7 models selected
> select add #19
9 models selected
> select add #20
11 models selected
> select add #21
13 models selected
> select add #22
15 models selected
> select add #25
17 models selected
> select add #24
19 models selected
> select add #23
21 models selected
> select add #26
23 models selected
> select add #27
25 models selected
> select add #28
27 models selected
> select add #29
29 models selected
> select add #30
31 models selected
> select add #31
34 models selected
> color #31.1#16.6.1 gray
> select subtract #16.6
31 models selected
> select subtract #17
29 models selected
> select subtract #18
27 models selected
> select subtract #19
25 models selected
> select subtract #20
23 models selected
> select subtract #21
21 models selected
> select subtract #22
19 models selected
> select subtract #23
17 models selected
> select subtract #24
15 models selected
> select subtract #25
13 models selected
> select subtract #26
11 models selected
> select subtract #27
9 models selected
> select subtract #28
7 models selected
> select subtract #29
5 models selected
> select subtract #30
3 models selected
> select subtract #31
Nothing selected
> volume #16.1 level 0.2264
> volume #16.2 level 0.1574
> volume #16.3 level 0.1808
> volume #16.4 level 0.1634
> volume #16.6 level 0.1084
> volume #16.6 color #0096ff
> volume #16.6 level 0.1506
> volume #16.5 level 0.322
> hide #!16.6 models
> hide #!16.5 models
> hide #!16.4 models
> hide #!16.3 models
> hide #!16.2 models
> hide #!16.1 models
> hide #!16 models
> show #!16.1 models
> hide #!16 models
> hide #!31 models
> hide #!16.1 models
> show #!16.2 models
> hide #!16.2 models
> show #!16.1 models
> show #!1 models
> volume resample #16.1 onGrid #16.6
Opened S2c.map resampled as #32, grid size 400,400,400, pixel 1.32, shown at
step 1, values float32
> volume resample #16.2 onGrid #16.6
Opened S2d.map resampled as #33, grid size 400,400,400, pixel 1.32, shown at
step 1, values float32
> volume resample #16.3 onGrid #16.6
Opened S2e.map resampled as #34, grid size 400,400,400, pixel 1.32, shown at
step 1, values float32
> volume resample #16.4 onGrid #16.6
Opened S2f.map resampled as #35, grid size 400,400,400, pixel 1.32, shown at
step 1, values float32
> volume resample #16.5 onGrid #16.6
Opened S2b.map resampled as #36, grid size 400,400,400, pixel 1.32, shown at
step 1, values float32
> volume morph #16.6,32-36
volume morph requires 2 or more volumes, got 1
> volume morph #32-36,16.6
volume morph requires 2 or more volumes, got 1
> hide #!16 models
> show #!16.1 models
> ui tool show "Side View"
> hide #!32 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> hide #!36 models
> hide #!16.1 models
> show #!16.2 models
> show #!16.3 models
> hide #!16.2 models
> show #!16.4 models
> hide #!16.3 models
> show #!16.5 models
> hide #!16.4 models
> show #!16.6 models
> hide #!16.5 models
> hide #!16.6 models
> show #!16.1 models
===== Log before crash end =====
Log:
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: 47 days, 17 hours, 2 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-maskChains: 1.4
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
Change History (2)
comment:1 by , 105 minutes ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 104 minutes ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Halle,
--Eric