![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17591 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 0x00000001fc3d8c80 (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, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.pdb._pdbio, chimerax.mlp._mlp (total: 53)
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{
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"procRole" : "Background",
"version" : 2,
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"modelCode" : "Mac16,8",
"coalitionID" : 6133,
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"build" : "24E263",
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"captureTime" : "2025-05-08 21:01:49.7116 +0200",
"codeSigningMonitor" : 2,
"incident" : "A9753AF1-D01F-4A3A-99A9-114542A7F8C8",
"pid" : 17345,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-07 00:13:17.7779 +0200",
"procStartAbsTime" : 1686600339393,
"procExitAbsTime" : 4016008741651,
"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":"C85AFF63-B670-5C0C-B85A-5EF44C466AC0","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "662A8EC1-317E-7F5A-75C7-E2DAA90C89DD",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage"]},
"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" : "63AA34BB-DE61-4A78-BDA0-28893665BEE9",
"wakeTime" : 18169,
"sleepWakeUUID" : "9D578C1D-4A0E-4219-8F54-C313CC1D80BB",
"sip" : "enabled",
"vmRegionInfo" : "0x343c7b6b89a8 is not in any region. Bytes after previous region: 56953336990121 Bytes before following region: 48118742939224\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, 0x0000343c7b6b89a8","rawCodes":[1,57434373327272],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000343c7b6b89a8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":17345},
"vmregioninfo" : "0x343c7b6b89a8 is not in any region. Bytes after previous region: 56953336990121 Bytes before following region: 48118742939224\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/christoph/Downloads/cryosparc_P262_J58_003_volume_map_sharp.mrc
Opened cryosparc_P262_J58_003_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 1.18, shown at level 0.356, step 2, values float32
> volume #1 step 1
> volume #1 level 0.4244
> volume #1 level 0.3745
> open /Users/christoph/Downloads/cryosparc_P262_J66_006_volume_map_sharp.mrc
Opened cryosparc_P262_J66_006_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.18, shown at level 0.369, step 2, values float32
> volume #2 step 1
> volume #2 level 0.6203
> volume #2 level 0.6251
> volume #2 level 0.5491
> volume #2 level 0.4873
> ui tool show "Side View"
> volume #2 level 0.2769
> open /Users/christoph/Downloads/cryosparc_P262_J70_006_volume_map_sharp.mrc
Opened cryosparc_P262_J70_006_volume_map_sharp.mrc as #3, grid size
360,360,360, pixel 1.18, shown at level 0.28, step 2, values float32
> volume #3 step 1
> volume #3 level 0.4288
> volume #2 level 0.4139
> ui tool show "Side View"
> volume #3 level 0.5514
> volume #3 level 0.4768
> volume #3 level 0.2477
> volume #3 level 0.221
> volume #2 level 0.1791
> open /Users/christoph/Downloads/cryosparc_P262_J67_class_04_00032_volume.mrc
Opened cryosparc_P262_J67_class_04_00032_volume.mrc as #4, grid size
100,100,100, pixel 3.78, shown at level 1.66, step 1, values float32
> open /Users/christoph/Downloads/cryosparc_P262_J67_class_03_00032_volume.mrc
Opened cryosparc_P262_J67_class_03_00032_volume.mrc as #5, grid size
100,100,100, pixel 3.78, shown at level 1.68, step 1, values float32
> open /Users/christoph/Downloads/cryosparc_P262_J67_class_02_00032_volume.mrc
Opened cryosparc_P262_J67_class_02_00032_volume.mrc as #6, grid size
100,100,100, pixel 3.78, shown at level 1.67, step 1, values float32
> volume #5 level 1.536
> volume #6 level 1.574
> volume #4 level 1.597
> volume #4 level 1.204
> volume #5 level 1.187
> volume #6 level 1.202
> open /Users/christoph/Downloads/cryosparc_P262_J88_007_volume_map_sharp.mrc
Opened cryosparc_P262_J88_007_volume_map_sharp.mrc as #7, grid size
360,360,360, pixel 1.18, shown at level 0.278, step 2, values float32
> volume #7 step 1
> volume #7 level 0.5022
> volume #7 level 0.4289
> volume #7 level 0.214
> volume #7 level 0.4143
> open /Users/christoph/Downloads/cryosparc_P262_J91_006_volume_map_sharp.mrc
Opened cryosparc_P262_J91_006_volume_map_sharp.mrc as #8, grid size
360,360,360, pixel 1.18, shown at level 0.291, step 2, values float32
> volume #8 level 0.4137
> volume #8 step 1
> open /Users/christoph/Downloads/cryosparc_P262_J126_008_volume_map_sharp.mrc
Opened cryosparc_P262_J126_008_volume_map_sharp.mrc as #9, grid size
360,360,360, pixel 1.18, shown at level 0.287, step 2, values float32
> volume #9 step 1
> volume #9 level 0.5577
> open /Users/christoph/Downloads/cryosparc_P262_J131_009_volume_map_sharp.mrc
Opened cryosparc_P262_J131_009_volume_map_sharp.mrc as #10, grid size
360,360,360, pixel 1.18, shown at level 0.404, step 2, values float32
> volume #10 step 1
> volume #10 level 0.7923
> volume #10 level 1.051
> volume #10 level 1.472
> open /Users/christoph/Downloads/cryosparc_P262_J131_010_volume_map_sharp.mrc
Opened cryosparc_P262_J131_010_volume_map_sharp.mrc as #11, grid size
360,360,360, pixel 1.18, shown at level 0.417, step 2, values float32
> volume #11 step 1
> volume #11 level 1.301
> volume #11 level 1.036
> volume #11 level 0.6293
> volume #11 level 0.4878
> volume #11 level 0.8239
> open "/Users/christoph/Downloads/cryosparc_P262_J163_011_volume_map_sharp
> (1).mrc"
Opened cryosparc_P262_J163_011_volume_map_sharp (1).mrc as #12, grid size
800,800,800, pixel 0.59, shown at step 1, values float32
> open "/Users/christoph/Downloads/cryosparc_P262_J163_011_volume_map_sharp
> (1).mrc"
Opened cryosparc_P262_J163_011_volume_map_sharp (1).mrc as #13, grid size
800,800,800, pixel 0.59, shown at step 1, values float32
> volume #12 level -0.03719,0 level 0.1385,0.8 level 0.7963,1
> volume #13 region 0,0,0,799,799,799 step 4
> volume #13
> volume #13 change image level -0.03719,0 level 0.1385,0.8 level 0.7963,1
> volume #13 step 1
> volume #13 step 2
> volume #13 level 0.2658
> volume #13 level 0.2266
> volume #13 level 0.1352
> volume #13 step 1
> ui tool show "Side View"
> volume #13 level 0.03722
> volume #13 level 0.07775
> volume #13 level 0.09126
> volume #13 level 0.1791
> close #12
> close #11
> close #10
> close #8
> close #7
> close #6
> close #5
> close #4
> close #3
> close #2
> close #1
> close #9
> open 3P05 fromDatabase pdb format mmcif
Summary of feedback from opening 3P05 fetched from pdb
---
notes | Fetching compressed mmCIF 3p05 from http://files.rcsb.org/download/3p05.cif
Fetching CCD IOD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IOD/IOD.cif
3p05 title:
X-ray structure of pentameric HIV-1 CA [more info...]
Chain information for 3p05 #1
---
Chain | Description | UniProt
A B C D E | HIV-1 CA | Q72497_9HIV1 1-231
Non-standard residues in 3p05 #1
---
IOD — iodide ion
> ui tool show "Side View"
> select add #1
7918 atoms, 8079 bonds, 7 pseudobonds, 1043 residues, 2 models selected
> ui mousemode right "translate selected atoms"
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,187.18,0,1,0,188.69,0,0,1,167.36
> ui mousemode right translate
> ui mousemode right "move picked models"
> rainbow sel
> color sel bypolymer
> color sel bychain
> mlp sel
Map values for surface "3p05_A SES surface": minimum -25.81, mean -4.541,
maximum 21.81
Map values for surface "3p05_B SES surface": minimum -26.05, mean -4.703,
maximum 22.75
Map values for surface "3p05_C SES surface": minimum -25.81, mean -4.473,
maximum 21.62
Map values for surface "3p05_D SES surface": minimum -25.81, mean -4.463,
maximum 22.95
Map values for surface "3p05_E SES surface": minimum -25.64, mean -4.484,
maximum 22.74
To also show corresponding color key, enter the above mlp command and add key
true
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> style sel stick
Changed 7918 atom styles
> view matrix models #13,1,0,0,6.3795,0,1,0,20.602,0,0,1,0.14904
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.75003,-0.21501,-0.62548,204.13,0.5855,0.65571,0.47669,170.19,0.30764,-0.72375,0.61769,171.2
> view matrix models
> #1,0.083348,0.59606,-0.7986,217.32,0.58009,0.6226,0.52524,169.19,0.81028,-0.50704,-0.29387,184.38
> view matrix models
> #1,-0.75364,0.54253,-0.37107,219.32,0.41403,0.8303,0.37307,174.86,0.5105,0.12753,-0.85037,200.88
> view matrix models
> #1,-0.58654,-0.47416,0.65662,194.16,-0.031378,0.82341,0.56658,176.67,-0.80932,0.31171,-0.49784,211.18
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.58654,-0.47416,0.65662,191.63,-0.031378,0.82341,0.56658,246.82,-0.80932,0.31171,-0.49784,198.86
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.4099,-0.04713,0.91091,183.88,-0.19222,0.9807,-0.035757,262.22,-0.89164,-0.18975,-0.41105,197.85
> view matrix models
> #1,-0.070684,0.54696,0.83417,181.22,-0.43545,0.73545,-0.51913,275.96,-0.89743,-0.39993,0.18619,184.8
> view matrix models
> #1,-0.14536,0.80884,0.56978,188.12,0.18106,0.58792,-0.7884,273.41,-0.97267,-0.011438,-0.2319,195.12
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.14536,0.80884,0.56978,167.55,0.18106,0.58792,-0.7884,269.94,-0.97267,-0.011438,-0.2319,208.34
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.56373,0.67103,0.48158,175.09,0.13201,0.64876,-0.74945,269.78,-0.81534,-0.35892,-0.45431,210.9
> view matrix models
> #1,-0.60855,0.64551,0.4615,176.12,0.12018,0.64986,-0.75049,269.96,-0.78436,-0.40125,-0.47305,210.87
> view matrix models
> #1,-0.57869,0.6445,0.49973,174.89,0.08611,0.65762,-0.74842,270.39,-0.81099,-0.39007,-0.43606,210.43
> view matrix models
> #1,-0.58727,0.64377,0.49058,175.2,0.093707,0.65611,-0.74882,270.29,-0.80395,-0.39379,-0.44564,210.54
> view matrix models
> #1,-0.57921,0.64621,0.49692,174.95,0.090478,0.65678,-0.74863,270.33,-0.81014,-0.38865,-0.43888,210.48
> view matrix models
> #1,-0.54385,0.66635,0.51011,174.2,0.10063,0.65526,-0.74867,270.19,-0.83313,-0.35583,-0.42342,210.47
> view matrix models
> #1,-0.51611,0.78916,0.33297,177.74,0.043544,0.41241,-0.90996,274.38,-0.85542,-0.45514,-0.24721,206.88
> fitmap #1 inMap #13
Fit molecule 3p05 (#1) to map cryosparc_P262_J163_011_volume_map_sharp (1).mrc
(#13) using 7918 atoms
average map value = 0.03009, steps = 100
shifted from previous position = 2.77
rotated from previous position = 2.78 degrees
atoms outside contour = 7002, contour level = 0.17908
Position of 3p05 (#1) relative to cryosparc_P262_J163_011_volume_map_sharp
(1).mrc (#13) coordinates:
Matrix rotation and translation
-0.53004435 0.79117044 0.30512671 172.33994883
0.08824897 0.40934533 -0.90810160 254.19453728
-0.84336534 -0.45440701 -0.28679115 209.97123240
Axis 0.31929971 0.80828201 -0.49469980
Axis point 110.10998301 0.00000000 151.21825395
Rotation angle (degrees) 134.72825071
Shift along axis 156.61624114
> fitmap #1 inMap #13
Fit molecule 3p05 (#1) to map cryosparc_P262_J163_011_volume_map_sharp (1).mrc
(#13) using 7918 atoms
average map value = 0.03009, steps = 44
shifted from previous position = 0.00189
rotated from previous position = 0.0104 degrees
atoms outside contour = 7004, contour level = 0.17908
Position of 3p05 (#1) relative to cryosparc_P262_J163_011_volume_map_sharp
(1).mrc (#13) coordinates:
Matrix rotation and translation
-0.53007904 0.79109207 0.30526962 172.33630051
0.08822141 0.40950805 -0.90803090 254.19310496
-0.84334642 -0.45439684 -0.28686290 209.97104744
Axis 0.31924459 0.80833755 -0.49464462
Axis point 110.11910378 0.00000000 151.20397659
Rotation angle (degrees) 134.72598108
Shift along axis 156.63021382
> fitmap #1 inMap #13
Fit molecule 3p05 (#1) to map cryosparc_P262_J163_011_volume_map_sharp (1).mrc
(#13) using 7918 atoms
average map value = 0.03009, steps = 80
shifted from previous position = 0.00122
rotated from previous position = 0.00276 degrees
atoms outside contour = 7002, contour level = 0.17908
Position of 3p05 (#1) relative to cryosparc_P262_J163_011_volume_map_sharp
(1).mrc (#13) coordinates:
Matrix rotation and translation
-0.53007878 0.79110902 0.30522613 172.33641867
0.08823626 0.40946603 -0.90804841 254.19264561
-0.84334503 -0.45440519 -0.28685376 209.97160116
Axis 0.31925829 0.80832435 -0.49465735
Axis point 110.11520593 0.00000000 151.20806058
Rotation angle (degrees) 134.72729633
Shift along axis 156.62593835
> fitmap #1 inMap #13
Fit molecule 3p05 (#1) to map cryosparc_P262_J163_011_volume_map_sharp (1).mrc
(#13) using 7918 atoms
average map value = 0.03008, steps = 48
shifted from previous position = 0.00393
rotated from previous position = 0.00646 degrees
atoms outside contour = 7001, contour level = 0.17908
Position of 3p05 (#1) relative to cryosparc_P262_J163_011_volume_map_sharp
(1).mrc (#13) coordinates:
Matrix rotation and translation
-0.53009737 0.79108361 0.30525972 172.33504475
0.08830057 0.40954650 -0.90800587 254.18775443
-0.84332661 -0.45437692 -0.28695266 209.97508210
Axis 0.31925648 0.80835589 -0.49460697
Axis point 110.11253002 0.00000000 151.20102043
Rotation angle (degrees) 134.72878945
Shift along axis 156.63811005
> ui mousemode right translate
> select subtract #1.2
6312 atoms, 6435 bonds, 6 pseudobonds, 833 residues, 7 models selected
> select subtract #1.3
4718 atoms, 4807 bonds, 5 pseudobonds, 624 residues, 6 models selected
> select subtract #1.5
3136 atoms, 3191 bonds, 3 pseudobonds, 418 residues, 5 models selected
> select subtract #1.4
1544 atoms, 1566 bonds, 2 pseudobonds, 209 residues, 4 models selected
> show sel atoms
> hide sel cartoons
> select add #1.5
3126 atoms, 1566 bonds, 2 pseudobonds, 415 residues, 3 models selected
> show sel atoms
> show sel cartoons
> hide sel cartoons
> select subtract #1.5
1544 atoms, 1566 bonds, 2 pseudobonds, 209 residues, 4 models selected
> select subtract #1.6
10 atoms, 10 residues, 2 models selected
> show sel atoms
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.5301,0.79108,0.30526,175.61,0.088301,0.40955,-0.90801,275.42,-0.84333,-0.45438,-0.28695,211.62
> ui mousemode right "rotate selected models"
> ui mousemode right rotate
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.5301,0.79108,0.30526,175.55,0.088301,0.40955,-0.90801,274.43,-0.84333,-0.45438,-0.28695,211.83
> fitmap #1 inMap #13
Fit molecule 3p05 (#1) to map cryosparc_P262_J163_011_volume_map_sharp (1).mrc
(#13) using 7918 atoms
average map value = 0.04867, steps = 136
shifted from previous position = 2.44
rotated from previous position = 9.92 degrees
atoms outside contour = 6791, contour level = 0.17908
Position of 3p05 (#1) relative to cryosparc_P262_J163_011_volume_map_sharp
(1).mrc (#13) coordinates:
Matrix rotation and translation
-0.51052697 0.79785208 0.32061544 168.66554053
-0.06358892 0.33681557 -0.93942094 256.81412590
-0.85750723 -0.49998732 -0.12121889 210.94136766
Axis 0.28830630 0.77294995 -0.56517949
Axis point 121.19115883 0.00000000 159.92626641
Rotation angle (degrees) 130.35075644
Shift along axis 127.91206826
> ui mousemode right translate
> ui mousemode right rotate
> hide #!13 models
> show #!13 models
> volume #13 style mesh
> color sel byhetero
> select add #1
7918 atoms, 8079 bonds, 7 pseudobonds, 1043 residues, 2 models selected
> color sel byhetero
> select subtract #1
5 models selected
> ui mousemode right translate
> ui mousemode right zoom
> open "/Users/christoph/Downloads/cryosparc_P262_J163_011_volume_map_sharp
> (1).mrc"
Opened cryosparc_P262_J163_011_volume_map_sharp (1).mrc as #2, grid size
800,800,800, pixel 0.59, shown at step 1, values float32
> ui mousemode right translate
> volume #2 level -0.03719,0 level 0.1385,0.8 level 0.7963,1
> volume #2 level -0.03719,0 level 0.08575,0.9471 level 0.7963,1
> volume #13 level 0.1692
> volume #13 level 0.1397
> volume #13 style surface
> volume #13 style mesh
> volume #2 region 0,0,0,799,799,799 step 4
> volume #2 step 1
> ui mousemode right zoom
> ui mousemode right translate
> ui tool show "Side View"
> volume #2 level 0.1748
> volume #2 step 2
> volume #2 step 1
> volume #2 level 0.1551
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right zoom
> volume #2 style surface
> volume #2 level 0.1781
> open /Users/christoph/Downloads/cryosparc_P262_J174_011_volume_map_sharp.mrc
Opened cryosparc_P262_J174_011_volume_map_sharp.mrc as #3, grid size
850,850,850, pixel 0.59, shown at step 1, values float32
> close #3
> open "/Users/christoph/Downloads/cryosparc_P262_J174_011_volume_map_sharp
> (1).mrc"
Opened cryosparc_P262_J174_011_volume_map_sharp (1).mrc as #3, grid size
850,850,850, pixel 0.59, shown at step 1, values float32
> volume #3 region 0,0,0,849,849,849 step 4
> volume #3 step 1
> volume #3 change image level -0.0977,0 level 0.3478,0.8 level 2.295,1
> volume #3 level 0.2765
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> volume #3 color #00fdff
===== 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/christoph/Downloads/cryosparc_P262_J174_011_volume_map_sharp
> (1).mrc"
Opened cryosparc_P262_J174_011_volume_map_sharp (1).mrc as #1, grid size
850,850,850, pixel 0.59, shown at step 1, values float32
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 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: Mac16,8
Model Number: Z1FF000HYD/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 48 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: 3 days, 12 hours, 27 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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 |
What we know about this ChimeraX crash was described in the bug report panel
"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."
The current ChimeraX release candidate and daily build use a newer Qt version that does not appear to have these crashes on multi-display Mac systems. You could try that.
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Reported by Christoph Kaiser