![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 5 months ago
#18028 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-15.5-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 0x00000001f154df00 (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, 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.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 56)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 2530,
"osVersion" : {
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-06-18 20:26:02.0324 -0400",
"codeSigningMonitor" : 1,
"incident" : "B18029AE-67D0-4F1D-BF62-9F9973C4E1E7",
"pid" : 42924,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-18 12:57:34.8666 -0400",
"procStartAbsTime" : 4593970726878,
"procExitAbsTime" : 5045468845303,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"1F210A2C-AA23-5746-A995-64425BC5C84B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "DB21C13B-D80C-314E-D035-48708297B8A8",
"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" : "1CDFE94F-25B9-4191-BDA7-5C6374DEC289",
"wakeTime" : 9,
"sleepWakeUUID" : "4CA0F527-A162-43E5-8810-7C4BCC2BFBD1",
"sip" : "enabled",
"vmRegionInfo" : "0xbad00000d14 is not in any region. Bytes after previous region: 12356620913941 Bytes before following region: 92715459015404\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, 0x00000bad00000d14","rawCodes":[1,12837657251092],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000bad00000d14"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":42924},
"vmregioninfo" : "0xbad00000d14 is not in any region. Bytes after previous region: 12356620913941 Bytes before following region: 92715459015404\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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===== 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/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingMaps/cryosparc_P18_J648_004_volume_map_sharp.mrc
Opened cryosparc_P18_J648_004_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.874, shown at level 0.0251, step 2, values float32
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingMaps/cryosparc_P18_J649_005_volume_map_sharp.mrc
Opened cryosparc_P18_J649_005_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.874, shown at level 0.02, step 2, values float32
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingMaps/cryosparc_P18_J650_003_volume_map_sharp.mrc
Opened cryosparc_P18_J650_003_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.874, shown at level 0.0206, step 2, values float32
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingMaps/cryosparc_P18_J651_003_volume_map_sharp.mrc
Opened cryosparc_P18_J651_003_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.874, shown at level 0.0237, step 2, values float32
> volume level 0.08
> volume step 1
> lighting soft
> set bgColor white
> ui mousemode right zoom
> surface dust #1-4
> hide #!4 models
> hide #!3 models
> hide #!2 models
> volume #1 level 0.06685
> volume #1 level 0.1162
> volume #1 level 0.1096
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!4 models
> hide #!3 models
> volume #4 level 0.1111
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> hide #!4 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.07457
> show #!3 models
> hide #!2 models
> volume #3 level 0.07018
> volume #3 level 0.08
> volume #4 level 0.09695
> volume #4 level 0.1421
> volume #4 level 0.1054
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/ConsensusMap/cryosparc_P18_J139_005_volume_map_sharp.mrc
Opened cryosparc_P18_J139_005_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.874, shown at level 0.025, step 2, values float32
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/ConsensusMap/cryosparc_P18_J211_mask.mrc
Opened cryosparc_P18_J211_mask.mrc as #6, grid size 320,320,320, pixel 0.874,
shown at level 0.552, step 2, values float32
> volume #5 step 1
> volume #5 color silver
> surface dust #5
> volume #5 level 0.101
> volume #6 step 1
> volume #6 level 1
> volume #5 level 0.09084
> volume #6 color #ffb2b280
> volume #6 color #ffb2b244
> volume #6 color #ff40ff21
> volume #5 level 0.101
> open /Users/yoojoong/Downloads/cryosparc_P18_J653_005_volume_map_sharp.mrc
Opened cryosparc_P18_J653_005_volume_map_sharp.mrc as #7, grid size
320,320,320, pixel 0.874, shown at level 0.02, step 2, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J652_005_volume_map_sharp.mrc
Opened cryosparc_P18_J652_005_volume_map_sharp.mrc as #8, grid size
320,320,320, pixel 0.874, shown at level 0.0242, step 2, values float32
> hide #!5 models
> hide #!6 models
> volume #7 step 1
> surface dust #7
> surface dust #8
> volume #7 level 0.07186
> volume #7 level 0.0932
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> volume #7 level 0.08101
> volume #8 level 0.07445
> volume #8 step 1
> volume #8 level 0.08623
> volume #8 level 0.1059
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingModels&Maps_SetB_BEST/28p1-TAS2R14_distant/28p1-TAS2R14_J534-0617-1250.pdb
Summary of feedback from opening
/Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
TAS2R14/Structure_work/WorkingModels&Maps_SetB_BEST/28p1-TAS2R14_distant/28p1-TAS2R14_J534-0617-1250.pdb
---
warning | Start residue of secondary structure not found: HELIX 23 23 ALA R 226 THR R 253 1 28
Chain information for 28p1-TAS2R14_J534-0617-1250.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
R | No description available
> fitmap #9/R inMap #8
Fit molecule 28p1-TAS2R14_J534-0617-1250.pdb (#9) to map
cryosparc_P18_J652_005_volume_map_sharp.mrc (#8) using 2187 atoms
average map value = 0.1869, steps = 84
shifted from previous position = 1.33
rotated from previous position = 6.78 degrees
atoms outside contour = 758, contour level = 0.10586
Position of 28p1-TAS2R14_J534-0617-1250.pdb (#9) relative to
cryosparc_P18_J652_005_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99461596 0.06954705 -0.07682642 -0.04549975
-0.07380060 0.99581071 -0.05398611 17.98318660
0.07275000 0.05936528 0.99558184 -16.84915917
Axis 0.47998289 -0.63337668 -0.60700117
Axis point 240.87500576 0.00000000 -10.07251714
Rotation angle (degrees) 6.78122423
Shift along axis -1.18451079
> hide atoms
> show cartoons
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingModels&Maps_SetB_BEST/28p1-TAS2R14_distant/RealSpaceRefine_191/28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb
Chain information for 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb
#10
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
R | No description available
> hide atoms
> show cartoons
> close #9
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingModels&Maps_SetB_BEST/28p1-TAS2R14_distant/RealSpaceRefine_191/28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb
Chain information for 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb
#9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
R | No description available
> close #9-10
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingModels&Maps_SetB_BEST/28p1-TAS2R14_distant/RealSpaceRefine_191/28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb
Chain information for 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb
#9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
R | No description available
> hide atoms
> show cartoons
> fitmap #9/R inMap #8
Fit molecule 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9) to
map cryosparc_P18_J652_005_volume_map_sharp.mrc (#8) using 2187 atoms
average map value = 0.1904, steps = 56
shifted from previous position = 1.46
rotated from previous position = 6.84 degrees
atoms outside contour = 730, contour level = 0.10586
Position of 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9)
relative to cryosparc_P18_J652_005_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99452369 0.06977472 -0.07780822 -0.00608448
-0.07412113 0.99576196 -0.05444425 18.15044176
0.07367963 0.05991333 0.99548064 -16.93844675
Axis 0.48012017 -0.63600838 -0.60413406
Axis point 240.12032438 0.00000000 -8.87235912
Rotation angle (degrees) 6.83973993
Shift along axis -1.31366162
> select ::name="LIG"
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!7 models
> hide #!8 models
> fitmap #9/R inMap #7
Fit molecule 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9) to
map cryosparc_P18_J653_005_volume_map_sharp.mrc (#7) using 2187 atoms
average map value = 0.1154, steps = 68
shifted from previous position = 2.36
rotated from previous position = 4.8 degrees
atoms outside contour = 1002, contour level = 0.081006
Position of 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9)
relative to cryosparc_P18_J653_005_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.98439139 0.13755504 -0.10978248 -4.49314176
-0.13968295 0.99012481 -0.01189657 21.19230270
0.10706193 0.02704562 0.99388444 -15.72800315
Axis 0.10996982 -0.61235235 -0.78289925
Axis point 143.24843282 47.99332997 0.00000000
Rotation angle (degrees) 10.19847420
Shift along axis -1.15782434
> volume #7 color #b2ffb275
> ui tool show "Side View"
> graphics silhouettes true
> show #!8 models
> hide #!7 models
> fitmap #9/R inMap #8
Fit molecule 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9) to
map cryosparc_P18_J652_005_volume_map_sharp.mrc (#8) using 2187 atoms
average map value = 0.1904, steps = 92
shifted from previous position = 2.36
rotated from previous position = 4.8 degrees
atoms outside contour = 732, contour level = 0.10586
Position of 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9)
relative to cryosparc_P18_J652_005_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99451707 0.06992912 -0.07775420 -0.02787968
-0.07426553 0.99575633 -0.05435039 18.15657562
0.07362356 0.05982684 0.99548999 -16.92905713
Axis 0.47931434 -0.63548166 -0.60532704
Axis point 240.09474832 0.00000000 -9.25115073
Rotation angle (degrees) 6.84043790
Shift along axis -1.30391796
> show #!1 models
> hide #!8 models
> fitmap #9/R inMap #1
Fit molecule 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9) to
map cryosparc_P18_J648_004_volume_map_sharp.mrc (#1) using 2187 atoms
average map value = 0.1527, steps = 92
shifted from previous position = 1.17
rotated from previous position = 16.7 degrees
atoms outside contour = 1055, contour level = 0.10959
Position of 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9)
relative to cryosparc_P18_J648_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.98409442 -0.12732080 0.12388534 4.96080326
0.12594467 0.99185704 0.01890923 -16.93231213
-0.12528409 -0.00300576 0.99211636 18.98394391
Axis -0.06156550 0.69998850 0.71149546
Axis point 143.34445587 21.70806724 0.00000000
Rotation angle (degrees) 10.25218590
Shift along axis 1.34915183
> volume #1 level 0.08251
> show #!8 models
> show #!7 models
> hide #!8 models
> volume #7 level 0.06881
> fitmap #9/R inMap #7
Fit molecule 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9) to
map cryosparc_P18_J653_005_volume_map_sharp.mrc (#7) using 2187 atoms
average map value = 0.1154, steps = 112
shifted from previous position = 3.36
rotated from previous position = 20.4 degrees
atoms outside contour = 840, contour level = 0.068812
Position of 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9)
relative to cryosparc_P18_J653_005_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.98439760 0.13747980 -0.10982108 -4.47632401
-0.13962283 0.99013167 -0.01203121 21.19866776
0.10708328 0.02717702 0.99387855 -15.75038681
Axis 0.11073358 -0.61259060 -0.78260516
Axis point 143.37305667 47.90042361 0.00000000
Rotation angle (degrees) 10.19731356
Shift along axis -1.15545005
> show #!8 models
> hide #!7 models
> fitmap #9/R inMap #8
Fit molecule 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9) to
map cryosparc_P18_J652_005_volume_map_sharp.mrc (#8) using 2187 atoms
average map value = 0.1904, steps = 80
shifted from previous position = 2.36
rotated from previous position = 4.8 degrees
atoms outside contour = 735, contour level = 0.10586
Position of 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9)
relative to cryosparc_P18_J652_005_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99452293 0.06980079 -0.07779448 -0.01228620
-0.07414687 0.99575970 -0.05445054 18.15514520
0.07366392 0.05992053 0.99548137 -16.93409481
Axis 0.48013842 -0.63583387 -0.60430322
Axis point 240.13241985 0.00000000 -8.94068313
Rotation angle (degrees) 6.84028985
Shift along axis -1.31622729
> fitmap #9/R inMap #7
Fit molecule 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9) to
map cryosparc_P18_J653_005_volume_map_sharp.mrc (#7) using 2187 atoms
average map value = 0.1154, steps = 68
shifted from previous position = 2.36
rotated from previous position = 4.8 degrees
atoms outside contour = 840, contour level = 0.068812
Position of 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9)
relative to cryosparc_P18_J653_005_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.98439948 0.13746383 -0.10982424 -4.47540784
-0.13961085 0.99013290 -0.01206827 21.20257494
0.10708165 0.02721266 0.99387776 -15.75305295
Axis 0.11094293 -0.61261720 -0.78255468
Axis point 143.40281744 47.89696418 0.00000000
Rotation angle (degrees) 10.19693882
Shift along axis -1.15795170
> show #!7 models
> hide #!8 models
> save
> /Users/yoojoong/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/3DVA/P18_J267_000_cls6/Classified6.cxs
> save
> /Users/yoojoong/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/3DVA/P18_J267_000_cls6/28p1-TAS2R14_J653.pdb relModel
> #7
> open /Users/yoojoong/Downloads/cryosparc_P18_J660_005_volume_map_sharp.mrc
Opened cryosparc_P18_J660_005_volume_map_sharp.mrc as #10, grid size
320,320,320, pixel 0.874, shown at level 0.0216, step 2, values float32
> hide #!7 models
> ui tool show "Side View"
> surface dust #10
> volume step 1 #10
Expected a keyword
> volume step 1
> volume level 0.08
> volume #10 level 0.09726
> fitmap #9 inMap #10
Fit molecule 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9) to
map cryosparc_P18_J660_005_volume_map_sharp.mrc (#10) using 8635 atoms
average map value = 0.06971, steps = 128
shifted from previous position = 4.62
rotated from previous position = 11.2 degrees
atoms outside contour = 6943, contour level = 0.097261
Position of 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9)
relative to cryosparc_P18_J660_005_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99981784 -0.01696141 0.00875206 1.12657269
0.01702193 0.99983139 -0.00688757 -0.84088456
-0.00863376 0.00703530 0.99993798 0.39454486
Axis 0.34265551 0.42788214 0.83636360
Axis point 58.93450530 58.59063844 0.00000000
Rotation angle (degrees) 1.16410858
Shift along axis 0.35620982
> fitmap #9/R inMap #10
Fit molecule 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9) to
map cryosparc_P18_J660_005_volume_map_sharp.mrc (#10) using 2187 atoms
average map value = 0.1493, steps = 44
shifted from previous position = 0.0972
rotated from previous position = 1.41 degrees
atoms outside contour = 920, contour level = 0.097261
Position of 28p1-TAS2R14_J534-0617-1250_real_space_refined_191.pdb (#9)
relative to cryosparc_P18_J660_005_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99919089 -0.03017017 0.02659568 0.92391474
0.03007368 0.99953960 0.00402059 -3.88224509
-0.02670474 -0.00321750 0.99963819 4.28480103
Axis -0.08962148 0.65996164 0.74593473
Axis point 141.62384962 28.46283705 0.00000000
Rotation angle (degrees) 2.31431609
Shift along axis 0.55124644
> volume #10 level 0.09036
> volume #10 level 0.08
> volume #10 level 0.09381
> show #!6 models
> volume #6 level 0.939
> volume #6 level 1
> volume #10 level 0.0869
> open /Users/yoojoong/Downloads/cryosparc_P18_J666_004_volume_map_sharp.mrc
Opened cryosparc_P18_J666_004_volume_map_sharp.mrc as #11, grid size
320,320,320, pixel 0.874, shown at level 0.0213, step 2, values float32
> volume #11 step 1
> volume #11 level 0.05304
> surface dust #11
> volume #11 level 0.07523
> volume #11 level 0.1006
> hide #!6 models
> open /Users/yoojoong/Downloads/cryosparc_P18_J655_008_volume_map.mrc
Opened cryosparc_P18_J655_008_volume_map.mrc as #12, grid size 320,320,320,
pixel 0.874, shown at level 0.0186, step 2, values float32
> volume #12 step 1
> volume #12 level 0.03098
> open /Users/yoojoong/Downloads/cryosparc_P18_J665_008_volume_map.mrc
Opened cryosparc_P18_J665_008_volume_map.mrc as #13, grid size 320,320,320,
pixel 0.874, shown at level 0.0187, step 2, values float32
> volume #13 step 1
> volume #13 level 0.02848
===== 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/yoojoong/Downloads/cryosparc_P18_J655_008_volume_map_sharp.mrc
Opened cryosparc_P18_J655_008_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.874, shown at level 0.0196, step 2, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J211_mask.mrc
Opened cryosparc_P18_J211_mask.mrc as #2, grid size 320,320,320, pixel 0.874,
shown at level 0.552, step 2, values float32
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
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: MacBookPro18,3
Model Number: MKGR3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 46 minutes, 45 seconds
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG ULTRAFINE:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
T24i-10:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
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-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
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 , 5 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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