![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17751 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x0000000206334c80 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.segment._segment (total: 64)
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"procRole" : "Background",
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"codeSigningMonitor" : 1,
"incident" : "767A4CFB-A02F-4049-8D36-E9DD1D6EB368",
"pid" : 22411,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-21 10:44:35.0907 +0200",
"procStartAbsTime" : 352705785449,
"procExitAbsTime" : 654806481010,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B362EAEC-D592-0B8A-05EB-D3BB388A7463",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "F19891BA-BDE1-4F38-A101-1E1A474A4E31",
"wakeTime" : 5416,
"sleepWakeUUID" : "ABB589A1-995F-485C-AEC0-C2EB3395F0BC",
"sip" : "enabled",
"vmRegionInfo" : "0x71d7624c86e8 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x000071d7624c86e8","rawCodes":[1,125169881089768],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000071d7624c86e8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":22411},
"vmregioninfo" : "0x71d7624c86e8 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
"name" : "_version.cpython-311-darwin.so"
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"uuid" : "87eed069-25fc-30f6-aa30-1e54859d92e2",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
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{
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"uuid" : "c1a3c2d3-b21b-3231-839d-fcbc83ca2028",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
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{
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"uuid" : "650aead6-ce16-39bb-9ba1-4bf9986b96d6",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
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"uuid" : "cc06500d-d418-3365-b197-36b1304a819e",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
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{
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"uuid" : "b32a8c32-a5e0-3a8b-9a0d-00a26b160215",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
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{
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"uuid" : "cd4f396b-89fe-36fd-a488-6f5b3d4b0282",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
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{
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"uuid" : "3133c77c-8bf7-32a3-b5db-cbfe2e50ce9d",
"path" : "\/Applications\/ChimeraX-1.9.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"
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{
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"uuid" : "de871a78-14f2-3e72-9bde-e4f2c7493f1b",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
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{
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"uuid" : "0c6e9a11-e483-3d7d-a88f-8ad0507af167",
"path" : "\/Applications\/ChimeraX-1.9.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"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.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"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
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"uuid" : "c8b24269-c8a2-3244-b044-b85c3449800d",
"path" : "\/Applications\/ChimeraX-1.9.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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{
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"arch" : "arm64",
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"uuid" : "f4191524-316f-3e56-8aa1-9a441a05fd70",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atom_search\/ast.cpython-311-darwin.so",
"name" : "ast.cpython-311-darwin.so"
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{
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"uuid" : "c6fd286f-9d33-37a1-9d00-a213039662b6",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/chem_group\/_chem_group.cpython-311-darwin.so",
"name" : "_chem_group.cpython-311-darwin.so"
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"uuid" : "f07c07fb-2e38-3764-9cff-1bd00023b5ae",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/coulombic\/_esp.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.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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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/annguyen/Downloads/cryosparc_P8_J115_003_volume_map.mrc
Opened cryosparc_P8_J115_003_volume_map.mrc as #1, grid size 250,250,250,
pixel 2.29, shown at level 0.4, step 1, values float32
> volume #1 level 0.2285
> ui tool show "Hide Dust"
> surface dust #1 size 13.75
> volume #1 level 0.1882
> open "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/13-02-25 fit TPR domian in map of RiboSec72.cxs" format session
Opened cryosparc_P26_J18_003_volume_map.mrc as #1, grid size 320,320,320,
pixel 1.34, shown at level 0.245, step 1, values float32
Opened cryosparc_P26_J18_003_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 1.34, shown at level 1.28, step 2, values float32
Opened cryosparc_P4_J508_007_volume_map.mrc as #15, grid size 432,432,432,
pixel 0.97, shown at level 0.469, step 1, values float32
Opened cryosparc_P4_J532_002_with particle substraction center.mrc as #16,
grid size 432,432,432, pixel 0.97, shown at level 0.0349, step 1, values
float32
Opened cryosparc_P4_J521_005_wo particle substraction side.mrc as #17, grid
size 432,432,432, pixel 0.97, shown at level 0.132, step 1, values float32
Opened cryosparc_P4_J527_005_wo particle substrction center.mrc as #18, grid
size 432,432,432, pixel 0.97, shown at level 0.132, step 1, values float32
Opened cryosparc_P4_J531_002_with particle substraction side.mrc as #19, grid
size 432,432,432, pixel 0.97, shown at level 0.0472, step 1, values float32
Opened emd_12977 map of 7old as #20, grid size 486,486,486, pixel 1.1, shown
at level 2.82, step 1, values float32
Opened cryosparc_P4_J627_004_volume_map.mrc as #21, grid size 432,432,432,
pixel 1.24, shown at level 0.134, step 1, values float32
opened ChimeraX session
> show #4 models
> show #2 models
> show #!15 models
> open "/Users/annguyen/ownCloud - Anh
> Nguyen@oc.biophys.mpg.de/Alphafold/AF-P39742-F1-model_v4-Yeast Sec72.pdb"
AF-P39742-F1-model_v4-Yeast Sec72.pdb title:
Alphafold monomer V2.0 prediction for translocation protein SEC72 (P39742)
[more info...]
Chain information for AF-P39742-F1-model_v4-Yeast Sec72.pdb #22
---
Chain | Description | UniProt
A | translocation protein SEC72 | SEC72_YEAST 1-193
Computing secondary structure
> show #!1 models
> show #!3 models
> hide #2 models
> hide #!3 models
> hide #4 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #2 models
> hide #2 models
> hide #!1 models
> show #!1 models
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_00_00011_volume.mrc
Opened J111_class_00_00011_volume.mrc as #23, grid size 100,100,100, pixel
5.73, shown at level 0.81, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_01_00011_volume.mrc
Opened J111_class_01_00011_volume.mrc as #24, grid size 100,100,100, pixel
5.73, shown at level 0.824, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_02_00011_volume.mrc
Opened J111_class_02_00011_volume.mrc as #25, grid size 100,100,100, pixel
5.73, shown at level 0.829, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_03_00011_volume.mrc
Opened J111_class_03_00011_volume.mrc as #26, grid size 100,100,100, pixel
5.73, shown at level 0.749, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_04_00011_volume.mrc
Opened J111_class_04_00011_volume.mrc as #27, grid size 100,100,100, pixel
5.73, shown at level 0.834, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_05_00011_volume.mrc
Opened J111_class_05_00011_volume.mrc as #28, grid size 100,100,100, pixel
5.73, shown at level 0.832, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_06_00011_volume.mrc
Opened J111_class_06_00011_volume.mrc as #29, grid size 100,100,100, pixel
5.73, shown at level 0.806, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_07_00011_volume.mrc
Opened J111_class_07_00011_volume.mrc as #30, grid size 100,100,100, pixel
5.73, shown at level 0.804, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_08_00011_volume.mrc
Opened J111_class_08_00011_volume.mrc as #31, grid size 100,100,100, pixel
5.73, shown at level 0.772, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_09_00011_volume.mrc
Opened J111_class_09_00011_volume.mrc as #32, grid size 100,100,100, pixel
5.73, shown at level 1.34e-06, step 1, values float32
> hide #!1 models
> hide #22 models
> select ~sel & ##selected
Nothing selected
> tile #23-32
9 models tiled
> volume #23-32 level 0.3
> tile #23-32 columns 10
9 models tiled
> open "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/18-05-25-scSec72-scRibo-10xbin.cxs" format session
Opened cryosparc_P8_J16_class_02_00042_volume.mrc as #2, grid size
128,128,128, pixel 4.48, shown at level 0.122, step 1, values float32
Opened cryosparc_P8_J16_class_03_00042_volume.mrc z flip as #3, grid size
128,128,128, pixel 4.48, shown at level 0.27, step 1, values float32
Opened cryosparc_P8_J16_class_00_00042_volume.mrc z flip as #5, grid size
128,128,128, pixel 4.48, shown at level 0.0367, step 1, values float32
Opened cryosparc_P5_J26_class_04_00042_volume.mrc as #1, grid size
128,128,128, pixel 4.48, shown at level 0.0781, step 1, values float32
opened ChimeraX session
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #4 models
> hide #!5 models
> hide #!1 models
> show #!2 models
> volume #2 color #ffffb2d9
> volume #2 color #ffffb2
> volume #2 color #ffffb2e6
> volume #2 color #ffffb2df
> hide #!2 models
> show #!3 models
> volume #3 color #9a6021eb
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #!5 models
> show #!2 models
> hide #!5 models
> volume #2 level 0.3904
> volume #2 level 0.301
> volume #2 level 0.2065
> volume gasussian #2 10
Expected a density maps specifier or a keyword
> hide #!2 models
> open
> /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_00_00011_volume.mrc
> format mrc
Opened J111_class_00_00011_volume.mrc as #7, grid size 100,100,100, pixel
5.73, shown at level 0.81, step 1, values float32
> hide #!7 models
> close #7
> show #!1 models
> show #!2 models
> open "/Users/annguyen/ownCloud - Anh
> Nguyen@oc.biophys.mpg.de/Alphafold/AF-P39742-F1-model_v4-Yeast Sec72.pdb"
AF-P39742-F1-model_v4-Yeast Sec72.pdb title:
Alphafold monomer V2.0 prediction for translocation protein SEC72 (P39742)
[more info...]
Chain information for AF-P39742-F1-model_v4-Yeast Sec72.pdb #7
---
Chain | Description | UniProt
A | translocation protein SEC72 | SEC72_YEAST 1-193
Computing secondary structure
> select add #7
1514 atoms, 1534 bonds, 193 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,495.18,0,1,0,-99.476,0,0,1,9.6755
> view matrix models #7,1,0,0,231.47,0,1,0,480.14,0,0,1,256.3
> hide #!1 models
> show #!3 models
> hide #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.63865,-0.4328,-0.63625,235.98,0.48176,0.86963,-0.10797,479.99,0.60003,-0.23757,0.76389,256.74
> view matrix models
> #7,0.26647,-0.52234,-0.81003,237.68,0.62173,0.73535,-0.26965,480.75,0.7365,-0.43177,0.52071,258
> view matrix models
> #7,-0.12223,-0.51154,-0.85052,238.58,0.66361,0.59511,-0.45329,481.8,0.73803,-0.61982,0.26673,259.56
> view matrix models
> #7,0.32752,-0.51535,-0.79193,237.46,0.60647,0.75737,-0.24204,480.6,0.72452,-0.40101,0.5606,257.78
> view matrix models
> #7,0.58645,-0.45325,-0.6713,236.29,0.50929,0.85079,-0.12953,480.08,0.62984,-0.26592,0.72978,256.9
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.58645,-0.45325,-0.6713,431.88,0.50929,0.85079,-0.12953,396.19,0.62984,-0.26592,0.72978,171.21
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.58795,-0.75187,-0.29834,432.35,0.76437,0.6371,-0.099217,396.58,0.26467,-0.1697,0.94929,170.98
> view matrix models
> #7,0.58614,-0.7671,-0.26076,432.34,0.78053,0.62094,-0.072189,396.56,0.21729,-0.16122,0.9627,171.01
> view matrix models
> #7,0.54838,-0.63874,-0.53971,432.52,0.61968,0.74377,-0.2506,396.77,0.56149,-0.19702,0.80368,170.84
> view matrix models
> #7,0.77014,-0.44972,-0.45237,430.9,0.40794,0.89244,-0.1927,396.37,0.49038,-0.03613,0.87076,170.05
> ui tool show "Fit in Map"
> fitmap #7 inMap #2
Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms
average map value = 0.1758, steps = 124
shifted from previous position = 20.9
rotated from previous position = 99.5 degrees
atoms outside contour = 990, contour level = 0.20645
Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates:
Matrix rotation and translation
-0.29566100 0.71916695 -0.62879525 191.95777257
0.76585194 -0.21500165 -0.60600750 317.20297658
-0.57101258 -0.66073685 -0.48720780 220.17597373
Axis -0.59314789 -0.62623923 0.50596443
Axis point -60.17408012 0.00000000 239.56782530
Rotation angle (degrees) 177.35574013
Shift along axis -201.10308507
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.082499,-0.77168,0.63064,415.47,0.57813,-0.5525,-0.60043,412.44,0.81177,0.31505,0.49171,172.22
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.57727,-0.81346,0.070915,418.19,0.45135,-0.39026,-0.80249,412.45,0.68047,-0.43125,0.59244,175.84
> view matrix models
> #7,0.5462,-0.63153,-0.55031,416.46,0.52948,0.76936,-0.35739,405.55,0.64909,-0.096171,0.75461,173.88
> view matrix models
> #7,0.68996,-0.69611,0.19848,414.53,0.36875,0.10206,-0.92391,410.57,0.62288,0.71064,0.32711,171.15
> view matrix models
> #7,0.76812,-0.62559,0.1365,414.18,0.11857,-0.070524,-0.99044,412.12,0.62923,0.77696,0.020005,171.6
> view matrix models
> #7,0.83432,-0.55118,0.010805,414,-0.19896,-0.31933,-0.92652,413.85,0.51413,0.77086,-0.37609,172.9
> view matrix models
> #7,0.99748,-0.028643,-0.064834,411.32,-0.069382,-0.20757,-0.97576,413.16,0.014492,0.9778,-0.20903,172.57
> view matrix models
> #7,0.99741,-0.027626,-0.066394,411.32,-0.070685,-0.20679,-0.97583,413.16,0.013229,0.97799,-0.20821,172.57
> view matrix models
> #7,0.86645,0.4971,0.046333,408.78,0.075331,-0.03843,-0.99642,412.08,-0.49354,0.86684,-0.070745,173.86
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.86645,0.4971,0.046333,411.37,0.075331,-0.03843,-0.99642,403.08,-0.49354,0.86684,-0.070745,173.25
> view matrix models
> #7,0.86645,0.4971,0.046333,411.44,0.075331,-0.03843,-0.99642,402.52,-0.49354,0.86684,-0.070745,172.13
> view matrix models
> #7,0.86645,0.4971,0.046333,414.95,0.075331,-0.03843,-0.99642,401.5,-0.49354,0.86684,-0.070745,165.96
> view matrix models
> #7,0.86645,0.4971,0.046333,417.5,0.075331,-0.03843,-0.99642,402.68,-0.49354,0.86684,-0.070745,169.59
> view matrix models
> #7,0.86645,0.4971,0.046333,422.13,0.075331,-0.03843,-0.99642,408.57,-0.49354,0.86684,-0.070745,166.36
> fitmap #7 inMap #2
Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms
average map value = 0.232, steps = 160
shifted from previous position = 37.6
rotated from previous position = 67.3 degrees
atoms outside contour = 588, contour level = 0.20645
Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates:
Matrix rotation and translation
-0.38395242 -0.31607344 0.86757024 205.45325374
-0.90522369 0.31412465 -0.28617437 336.34493386
-0.18207308 -0.89522248 -0.40672608 204.21922377
Axis -0.45148270 0.77809256 -0.43673258
Axis point 259.91409793 0.00000000 136.29485618
Rotation angle (degrees) 137.58484244
Shift along axis 79.75971298
> undo
> view matrix models
> #7,0.86645,0.4971,0.046333,421.36,0.075331,-0.03843,-0.99642,404.49,-0.49354,0.86684,-0.070745,166.07
> view matrix models
> #7,0.86645,0.4971,0.046333,411.19,0.075331,-0.03843,-0.99642,411.72,-0.49354,0.86684,-0.070745,165.57
> view matrix models
> #7,0.86645,0.4971,0.046333,419.69,0.075331,-0.03843,-0.99642,403.55,-0.49354,0.86684,-0.070745,162.35
> view matrix models
> #7,0.86645,0.4971,0.046333,419.72,0.075331,-0.03843,-0.99642,402.58,-0.49354,0.86684,-0.070745,161.28
> view matrix models
> #7,0.86645,0.4971,0.046333,419.57,0.075331,-0.03843,-0.99642,402.67,-0.49354,0.86684,-0.070745,161.48
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.79617,0.26645,-0.54325,422.35,-0.60073,0.45544,-0.65703,400.9,0.072354,0.84946,0.52267,158.8
> view matrix models
> #7,-0.38844,0.37591,-0.84131,425.18,-0.21376,0.85134,0.47909,395.22,0.89634,0.36594,-0.25034,161.32
> view matrix models
> #7,0.33812,-0.38844,-0.8572,427.32,-0.89862,-0.40382,-0.17147,404.44,-0.27955,0.82828,-0.4856,162.27
> view matrix models
> #7,0.52121,0.84885,-0.088332,418.98,0.35469,-0.30959,-0.88224,403.08,-0.77623,0.4285,-0.46244,165.22
> view matrix models
> #7,0.49381,-0.38603,-0.77919,426.77,-0.86755,-0.27978,-0.4112,404.39,-0.059272,0.87904,-0.47306,161.51
> view matrix models
> #7,0.9219,0.35032,-0.16545,420.7,0.33619,-0.93561,-0.10772,404.14,-0.19254,0.043681,-0.98032,167.13
> view matrix models
> #7,0.97842,0.17461,-0.11046,421.29,0.14939,-0.96717,-0.20558,404.96,-0.14273,0.18464,-0.97239,166.32
> volume #2 level 0.1593
> view matrix models
> #7,0.6461,0.76091,0.059758,418.75,0.6641,-0.52184,-0.5354,402.53,-0.37621,0.38561,-0.84248,165.53
> view matrix models
> #7,0.72813,0.67826,0.098929,418.87,0.61827,-0.58759,-0.522,402.92,-0.29592,0.44125,-0.84719,165.1
> view matrix models
> #7,0.62815,0.32171,-0.70847,422.88,-0.77253,0.14917,-0.61721,402.65,-0.092884,0.93501,0.34223,159.22
> fitmap #7 inMap #2
Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms
average map value = 0.2074, steps = 92
shifted from previous position = 29.9
rotated from previous position = 17.3 degrees
atoms outside contour = 527, contour level = 0.15934
Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates:
Matrix rotation and translation
-0.38172565 -0.71830578 0.58165482 198.20909708
-0.89890758 0.43494493 -0.05280216 329.00225981
-0.21505972 -0.54300987 -0.81172015 214.28905460
Axis -0.51453513 0.83625290 -0.18956448
Axis point 236.60478304 0.00000000 104.05931239
Rotation angle (degrees) 151.55207606
Shift along axis 132.52195625
> view matrix models
> #7,0.29815,0.75481,-0.58426,403.08,-0.94016,0.12647,-0.31639,419.06,-0.16492,0.64363,0.74735,177.75
> view matrix models
> #7,-0.4415,0.89545,0.056978,402.37,0.55832,0.22446,0.79869,412.45,0.7024,0.38443,-0.59904,180.56
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for AF-P39742-F1-model_v4-Yeast Sec72.pdb_A SES surface #7.1:
minimum, -17.75, mean -1.54, maximum 10.72
To also show corresponding color key, enter the above coulombic command and
add key true
> view matrix models
> #7,-0.055832,0.99656,0.061312,400.93,0.54606,-0.020933,0.83749,413.58,0.83589,0.080238,-0.54301,181.59
> view matrix models
> #7,-0.60166,0.79615,0.064393,403.22,0.52887,0.33666,0.77907,412.02,0.59858,0.50279,-0.62362,180.3
> view matrix models
> #7,-0.16521,0.98459,0.057397,401.26,0.5596,0.045658,0.8275,413.25,0.81213,0.16883,-0.55852,181.26
> view matrix models
> #7,-0.55223,0.83143,0.06136,402.94,0.54075,0.3012,0.78541,412.15,0.63453,0.4669,-0.61593,180.37
> view matrix models
> #7,-0.19703,0.97876,0.056635,401.37,0.56213,0.065453,0.82446,413.15,0.80324,0.19428,-0.56309,181.16
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.19703,0.97876,0.056635,417.45,0.56213,0.065453,0.82446,399.43,0.80324,0.19428,-0.56309,168.22
> view matrix models
> #7,-0.19703,0.97876,0.056635,419.8,0.56213,0.065453,0.82446,398.11,0.80324,0.19428,-0.56309,167.29
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.62471,0.2148,-0.75073,423.14,-0.72578,0.51439,-0.45677,401.7,0.28805,0.83022,0.47724,163.34
> view matrix models
> #7,0.076393,0.91561,0.39474,418.74,0.98476,-0.13133,0.11405,399.48,0.15626,0.38001,-0.91169,168.68
> show #!6 models
> view matrix models
> #7,-0.40791,0.85234,0.32732,420.37,0.89861,0.31133,0.30915,397.15,0.1616,0.42024,-0.89291,168.43
> view matrix models
> #7,0.62067,0.26302,-0.73864,422.89,-0.72586,0.54897,-0.41444,401.45,0.29649,0.79338,0.53164,163.38
> view matrix models
> #7,0.787,0.4945,-0.36892,420.61,-0.57145,0.80967,-0.13375,399.24,0.23257,0.31608,0.91979,165.05
> view matrix models
> #7,0.64509,0.28852,-0.70754,422.65,-0.3065,0.94592,0.10628,397.44,0.69994,0.1483,0.69863,165.18
> view matrix models
> #7,0.97784,0.073831,-0.19589,421.82,0.045789,0.83766,0.54428,396.21,0.20428,-0.54119,0.81571,169.47
> view matrix models
> #7,0.87693,-0.22396,-0.42525,423.98,0.40975,0.81081,0.41796,395.71,0.25119,-0.54077,0.80279,169.38
> view matrix models
> #7,0.56262,0.041042,-0.82569,424.28,0.064642,0.99353,0.093431,396.33,0.82418,-0.10594,0.55633,166.39
> fitmap #7 inMap #2
Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms
average map value = 0.1998, steps = 164
shifted from previous position = 38.2
rotated from previous position = 52.9 degrees
atoms outside contour = 574, contour level = 0.15934
Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates:
Matrix rotation and translation
-0.99704805 0.00838735 -0.07632046 205.41510085
-0.06490415 0.43898253 0.89614830 333.43347542
0.04101965 0.89845645 -0.43714231 209.14419648
Axis 0.01668121 -0.84802994 -0.52968572
Axis point 105.93579805 0.00000000 4.76705404
Rotation angle (degrees) 176.03288284
Shift along axis -390.11569049
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.95276,0.093927,-0.28883,413.68,0.14353,0.69886,0.70071,402.81,0.26767,-0.70906,0.65237,170.71
> view matrix models
> #7,0.95276,0.093927,-0.28883,415.53,0.14353,0.69886,0.70071,403.48,0.26767,-0.70906,0.65237,170.06
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.4107,-0.42511,-0.80661,420.42,0.38014,-0.72427,0.57526,410.04,-0.82875,-0.54288,-0.13586,173.54
> fitmap #7 inMap #2
Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms
average map value = 0.5909, steps = 152
shifted from previous position = 75.6
rotated from previous position = 53.2 degrees
atoms outside contour = 189, contour level = 0.15934
Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates:
Matrix rotation and translation
-0.36537732 0.82900503 0.42337935 253.70171638
0.67542842 -0.07686771 0.73340834 343.65826821
0.64054340 0.55393322 -0.53184784 200.71086084
Axis -0.55933969 -0.67679840 -0.47862620
Axis point -13.69521201 0.00000000 -21.72737954
Rotation angle (degrees) 170.76786469
Shift along axis -470.55828152
> undo
> view matrix models
> #7,0.67451,0.27265,-0.68608,416.16,-0.71574,0.46932,-0.51716,409.18,0.18099,0.83988,0.51171,163.07
> fitmap #7 inMap #2
Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms
average map value = 0.2074, steps = 80
shifted from previous position = 19.8
rotated from previous position = 11.4 degrees
atoms outside contour = 526, contour level = 0.15934
Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates:
Matrix rotation and translation
-0.38026206 -0.71895260 0.58181434 198.23758393
-0.89952691 0.43377184 -0.05189727 329.06031594
-0.21506299 -0.54309222 -0.81166418 214.34129831
Axis -0.51522568 0.83586297 -0.18940855
Axis point 236.86349273 0.00000000 104.02709263
Rotation angle (degrees) 151.53124705
Shift along axis 132.31416225
> view matrix models
> #7,0.20052,0.3051,-0.93097,406.31,-0.91895,0.38797,-0.070785,417.39,0.33959,0.86971,0.35817,176.36
> view matrix models
> #7,0.42815,0.34344,-0.83591,405.37,-0.90043,0.24089,-0.36222,418.66,0.076957,0.90776,0.41238,176.7
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.42815,0.34344,-0.83591,407.73,-0.90043,0.24089,-0.36222,401.27,0.076957,0.90776,0.41238,151.51
> view matrix models
> #7,0.42815,0.34344,-0.83591,405.33,-0.90043,0.24089,-0.36222,407.53,0.076957,0.90776,0.41238,153.19
> view matrix models
> #7,0.42815,0.34344,-0.83591,412.88,-0.90043,0.24089,-0.36222,414.29,0.076957,0.90776,0.41238,160.47
> view matrix models
> #7,0.42815,0.34344,-0.83591,413.05,-0.90043,0.24089,-0.36222,414.28,0.076957,0.90776,0.41238,160.13
> fitmap #7 inMap #2
Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms
average map value = 0.2074, steps = 84
shifted from previous position = 19
rotated from previous position = 11.2 degrees
atoms outside contour = 524, contour level = 0.15934
Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates:
Matrix rotation and translation
-0.38228232 -0.71820425 0.58141454 198.20777711
-0.89867229 0.43540176 -0.05304159 328.99776277
-0.21505421 -0.54277801 -0.81187666 214.27532541
Axis -0.51429597 0.83641048 -0.18951825
Axis point 236.50941442 0.00000000 104.06276879
Rotation angle (degrees) 151.56749759
Shift along axis 132.63063037
> view matrix models
> #7,0.55184,0.40864,-0.72697,445.4,-0.82916,0.36216,-0.42584,386.56,0.089261,0.83777,0.53868,145.48
> save "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/18-05-25-scSec72-scRibo-10xbin.cxs"
> open
> /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_00_00018_volume.mrc
Opened J110_class_00_00018_volume.mrc as #8, grid size 100,100,100, pixel
5.73, shown at level 0.794, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_01_00018_volume.mrc
Opened J110_class_01_00018_volume.mrc as #9, grid size 100,100,100, pixel
5.73, shown at level 0.839, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_02_00018_volume.mrc
Opened J110_class_02_00018_volume.mrc as #10, grid size 100,100,100, pixel
5.73, shown at level 0.805, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_03_00018_volume.mrc
Opened J110_class_03_00018_volume.mrc as #11, grid size 100,100,100, pixel
5.73, shown at level 0.806, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_04_00018_volume.mrc
Opened J110_class_04_00018_volume.mrc as #12, grid size 100,100,100, pixel
5.73, shown at level 0.813, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_05_00018_volume.mrc
Opened J110_class_05_00018_volume.mrc as #13, grid size 100,100,100, pixel
5.73, shown at level 0.778, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_06_00018_volume.mrc
Opened J110_class_06_00018_volume.mrc as #14, grid size 100,100,100, pixel
5.73, shown at level 0.775, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_07_00018_volume.mrc
Opened J110_class_07_00018_volume.mrc as #15, grid size 100,100,100, pixel
5.73, shown at level 0.816, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_08_00018_volume.mrc
Opened J110_class_08_00018_volume.mrc as #16, grid size 100,100,100, pixel
5.73, shown at level 0.794, step 1, values float32
> open
> /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_09_00018_volume.mrc
Opened J110_class_09_00018_volume.mrc as #17, grid size 100,100,100, pixel
5.73, shown at level 0.818, step 1, values float32
> hide #!6 models
> hide #!7 models
> select subtract #7
1 model selected
> hide #!2 models
> tile columns 5 rows 2 models #8-17
Expected a keyword
> tile columns 5 rows 2 models #8-17
Expected a keyword
> hide ~
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> tile columns 5 rows 2
Expected a keyword
> modeldisplay #8-17
Unknown command: modeldisplay #8-17
> tile columns 5 rows 2
Expected a keyword
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!11 models
> show #!8 models
> show #!9 models
> hide #!9 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> volume #11 level 0.4579
> volume #12 level 0.3937
> volume #13 level 0.4076
> volume #14 level 0.4802
> volume #15 level 0.4586
> volume #16 level 0.4684
> volume #17 level 0.4663
> show #!8 models
> volume #8 level 0.4239
> volume #9 level 0.5066
> volume gaussian #9 sDev 4
Opened J110_class_01_00018_volume.mrc gaussian as #18, grid size 100,100,100,
pixel 5.73, shown at step 1, values float32
> undo
> close #18
> volume gaussian #9 sDev 9
Opened J110_class_01_00018_volume.mrc gaussian as #18, grid size 100,100,100,
pixel 5.73, shown at step 1, values float32
> volume gaussian #9 sDev 6
Opened J110_class_01_00018_volume.mrc gaussian as #19, grid size 100,100,100,
pixel 5.73, shown at step 1, values float32
> close #18
> volume #19 level 0.3162
> close #19
> volume gaussian #9 sDev 5
Opened J110_class_01_00018_volume.mrc gaussian as #18, grid size 100,100,100,
pixel 5.73, shown at step 1, values float32
> volume #18 level 0.2342
> ui tool show "Segment Map"
Segmenting J110_class_01_00018_volume.mrc gaussian, density threshold 0.234190
Showing 15 region surfaces
235 watershed regions, grouped to 15 regions
Showing J110_class_01_00018_volume gaussian.seg - 15 regions, 15 surfaces
> undo
> close #19
> hide #!10 models
> volume save ~/Desktop/mask_60S.mrc #18
Expected a density maps specifier or a keyword
> volume save ~/Desktop/mask_60S.mrc models #18
Expected a density maps specifier or a keyword
> info models #18
model id #18 type Volume name "J110_class_01_00018_volume.mrc gaussian"
model id #18.1 type VolumeSurface name surface
> volume save ~/Desktop/mask_60S.mrc map #18
Expected a density maps specifier or a keyword
> volume save ~/Desktop/mask_60S.mrc
Expected a density maps specifier or a keyword
> hide #!10 models
> volume save ~/Desktop/mask_60S.mrc
Expected a density maps specifier or a keyword
> volume #18 level 0.1919
> volume #18 level 0.18
> volume #18 level 0.19
> hide #!18 models
> show #!9 models
> volume #9 level 0.8736
> hide #!9 models
> show #!18 models
> show #!9 models
> volume gaussian #9 sDev 4
Opened J110_class_01_00018_volume.mrc gaussian as #19, grid size 100,100,100,
pixel 5.73, shown at step 1, values float32
> hide #!18 models
> volume #19 level 0.3912
> volume #19 level 0.3064
> ui tool show "Segment Map"
Segmenting J110_class_01_00018_volume.mrc gaussian, density threshold 0.306386
Showing 14 region surfaces
300 watershed regions, grouped to 14 regions
Showing J110_class_01_00018_volume gaussian.seg - 14 regions, 14 surfaces
> volume #19 level 0.2126
> hide #!19 models
> show #!19 models
> hide #!19 models
Drag select of 402, 3000 of 45968 triangles, 400, 391, 96 of 176 triangles,
143
> view matrix models
> #20.1,1,0,0,-107.1,0,1,0,78.908,0,0,1,451.03,#20.3,1,0,0,-107.1,0,1,0,78.908,0,0,1,451.03,#20.7,1,0,0,-107.1,0,1,0,78.908,0,0,1,451.03,#20.14,1,0,0,-107.1,0,1,0,78.908,0,0,1,451.03
Drag select of 399, 401, 291, 148 of 160 triangles, 61, 289, 43 of 44
triangles, 158
> select clear
Drag select of 398, 401, 291, 396, 61, 287, 158
Deleted 7 regions
Drag select of 399, 300, 289
Deleted 3 regions
Showing 4 region surfaces
> hide #!20 models
> show #!20 models
Drag select of 402, 344 of 45968 triangles, 400, 391, 143
Drag select of 402, 161 of 45968 triangles, 400, 391, 143
Drag select of 400, 276 of 316 triangles, 391, 166 of 176 triangles, 143
Deleted 3 regions
> open /Users/annguyen/Downloads/cryosparc_P8_J123_001_volume_map.mrc
Opened cryosparc_P8_J123_001_volume_map.mrc as #21, grid size 250,250,250,
pixel 2.29, shown at level 0.226, step 1, values float32
> hide #!20 models
> volume #21 level 0.008316
> ui tool show "Side View"
> volume #21 level 0.1258
> volume #21 level 0.08917
> volume #21 level 0.1319
> close #21
> show #!20 models
Saving 1 regions to mrc file...
Opened mask_60S.mrc as #21, grid size 68,51,62, pixel 5.73, shown at step 1,
values float32
Wrote mask_60S.mrc
> volume #21 level 0.3666
> volume resample #21 onGrid #1
Opened mask_60S.mrc resampled as #22, grid size 128,128,128, pixel 4.48, shown
at step 1, values float32
> volume resample #21 onGrid #9
Opened mask_60S.mrc resampled as #23, grid size 100,100,100, pixel 5.73, shown
at step 1, values float32
> save /Users/annguyen /Desktop/60S_mask_resample128.mrc #22
Cannot determine format for '/Users/annguyen'
> save /Users/annguyen/Desktop/60S_mask_resample128.mrc #22
> save /Users/annguyen/Desktop/60S_mask_resample100.mrc #23
> hide #!20 models
> hide #!22 models
> hide #!23 models
> show #!23 models
> show #!9 models
> hide #!23 models
> volume copy #9
Opened J110_class_01_00018_volume.mrc copy as #24, grid size 100,100,100,
pixel 5.73, shown at step 1, values float32
> volume #24 level 0.5002
> close #24
> close #23
> show #!22 models
> ui tool show "Side View"
> volume #22 level 0.5978
> volume #22 level 1.008
> close #22
> show #!21 models
> ui mousemode right "map eraser"
> volume #21 level 0.3895
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> volume erase #21 center 366.49,382.85,188.29 radius 47.926
> volume erase #21 center 414.79,314.84,262.52 radius 47.926
> volume erase #21 center 380,207.63,280.69 radius 34.873
> volume erase #21 center 377.45,206.56,278.46 radius 34.873
> volume erase #21 center 414.77,268.23,315.92 radius 34.873
> volume erase #21 center 342.16,390.7,312.31 radius 34.873
> volume erase #21 center 327.15,404.07,300.25 radius 34.873
> volume erase #21 center 311.52,413.31,270.86 radius 34.873
> volume erase #21 center 331.81,371.6,435.54 radius 34.873
> volume erase #21 center 363.69,370.71,340.24 radius 34.873
> volume erase #21 center 411.47,344.75,295.78 radius 34.873
> volume erase #21 center 326.97,410.67,238.63 radius 34.873
> volume erase #21 center 291.82,422.85,276.21 radius 34.873
> volume erase #21 center 302.06,399.23,336.25 radius 34.873
> volume erase #21 center 391.69,329.81,350.06 radius 34.873
> volume erase #21 center 277.23,431.84,247.82 radius 34.873
> volume erase #21 center 241.97,413.04,254.94 radius 34.873
> volume #21 level 0.3601
> volume erase #21 center 378.08,372.05,278.19 radius 34.873
> volume erase #21 center 353.27,368.85,289.09 radius 34.873
> volume erase #21 center 300.53,327.59,452.97 radius 34.873
> volume resample #21 onGrid #9
Opened mask_60S.mrc resampled as #23, grid size 100,100,100, pixel 5.73, shown
at step 1, values float32
> volume resample #21 onGrid #1
Opened mask_60S.mrc resampled as #24, grid size 128,128,128, pixel 4.48, shown
at step 1, values float32
> rename #23 "mask_60S.mrc resampledb 100"
> rename #23 "mask_60S.mrc resampled 100"
> rename #24 "mask_60S.mrc resampled 120"
> save /Users/annguyen/Desktop/60S_mask_resample100.mrc #23
> save /Users/annguyen/Desktop/60S_mask_resample128.mrc #24
> volume #23 level 0.3994
> volume #24 level 0.3539
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/annguyen/Downloads/cryosparc_P8_J137_mask.mrc
Opened cryosparc_P8_J137_mask.mrc as #1, grid size 128,128,128, pixel 4.48,
shown at level 1, step 1, values float32
> open /Users/annguyen/Downloads/cryosparc_P8_J137_mask.mrc
Opened cryosparc_P8_J137_mask.mrc as #2, grid size 128,128,128, pixel 4.48,
shown at level 1, step 1, values float32
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16U000NJD/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 21 hours, 4 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
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 P3223QE:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.1
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
finufft: 2.3.1
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 months ago
| 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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