![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 weeks ago
Closed 8 weeks ago
#18623 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: 1.10 (2025-06-26 08:57:52 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 0x00000001fd6c5f00 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 52)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,1",
"coalitionID" : 4088,
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-08-25 17:36:56.2989 -0700",
"codeSigningMonitor" : 2,
"incident" : "CE20B20D-13A8-4477-9A39-B7ABD26A452D",
"pid" : 43001,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-25 13:37:16.1803 -0700",
"procStartAbsTime" : 2709655880144,
"procExitAbsTime" : 3054760588531,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0FA0117C-B405-5790-A016-320129310CE0","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D97943DC-6DFD-31A3-C756-1C3DDF53D08C",
"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" : "7B9DDE21-5E67-4298-8812-0B66C519DC88",
"wakeTime" : 31246,
"sleepWakeUUID" : "B58B8466-FF86-46BC-AF3A-149227A15120",
"sip" : "enabled",
"vmRegionInfo" : "0x6b664b0c8a70 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, 0x00006b664b0c8a70","rawCodes":[1,118087089949296],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00006b664b0c8a70"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":43001},
"vmregioninfo" : "0x6b664b0c8a70 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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"faultingThread" : 0,
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"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6723555328,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 14586624,
"uuid" : "e8f6a451-0acc-3e05-b18f-fec6618ce44a",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3502.1.401"
}
],
"sharedCache" : {
"base" : 6695436288,
"size" : 5047205888,
"uuid" : "d7397d7f-8df9-3920-81a7-c0a144be9c51"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=3.5G written=85.2M(2%) resident=2131K(0%) swapped_out=83.1M(2%) unallocated=3.4G(98%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 2672K 57 \nColorSync 720K 37 \nCoreAnimation 2928K 158 \nCoreGraphics 64K 4 \nCoreServices 624K 2 \nCoreUI image data 5472K 39 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.8G 117 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 576K 36 \nStack 199.2M 37 \nStack Guard 56.0M 1 \nVM_ALLOCATE 294.7M 233 \nVM_ALLOCATE (reserved) 160.0M 3 reserved VM address space (unallocated)\n__AUTH 5521K 697 \n__AUTH_CONST 77.4M 944 \n__CTF 824 1 \n__DATA 37.1M 1074 \n__DATA_CONST 37.0M 1092 \n__DATA_DIRTY 2778K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 645.3M 142 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1110 \n__TEXT (graphics) 288K 2 \n__TPRO_CONST 128K 2 \ndyld private memory 1200K 10 \nmapped file 654.4M 101 \npage table in kernel 2131K 1 \nshared memory 3280K 29 \n=========== ======= ======= \nTOTAL 6.3G 6306 \nTOTAL, minus reserved VM space 6.2G 6306 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "f303680ab7ff50321ccb0df7248e729e19344f84",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5f72dc58705eff005a46b3a9",
"factorPackIds" : {
},
"deploymentId" : 240000015
},
{
"rolloutId" : "67181b10c68c361a728c7cfa",
"factorPackIds" : {
},
"deploymentId" : 240000005
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/mariarafiq/Documents/SLC33/IXA4C/Phenix/Deposition/pdb_submitted/IXA4.pdb
Chain information for IXA4.pdb #1
---
Chain | Description
A | No description available
> open /Users/mariarafiq/Documents/SLC33/Ixa4/Phenix/J277_aligned_topdb.mrc
Opened J277_aligned_topdb.mrc as #2, grid size 256,256,256, pixel 0.727, shown
at level 0.0418, step 1, values float32
> volume #2 level 0.07587
> color #2 #dc6af5ff models
> color #2 salmon models
> lighting soft
> color #2 #ef9a55ff models
> camera ortho
> volume #2 level 0.08252
> hide #!2 models
> select add #1
7383 atoms, 7493 bonds, 2 pseudobonds, 445 residues, 2 models selected
> select /A
7383 atoms, 7493 bonds, 2 pseudobonds, 445 residues, 2 models selected
> color (#!1 & sel) light gray
> show #!2 models
> select ::name="LIG"
60 atoms, 62 bonds, 1 residue, 1 model selected
> color sel forest green
> select ::name="Y01"
252 atoms, 261 bonds, 3 residues, 1 model selected
> color sel dim gray
> ui tool show "Color Zone"
> color zone #2 near #1 distance 4.36
> color single #2
Need to color zone map before it can be split
> color zone #2 near #1 distance 6
> color zone #2 near #1 distance 9
> select ::name="Y01"
252 atoms, 261 bonds, 3 residues, 1 model selected
> color sel magenta
> color zone #2 near #1 distance 9
> color zone #2 near #1 distance 8
> color zone #2 near #1 distance 6
> color zone #2 near #1 distance 4
> hide #!2 models
> select /A
7383 atoms, 7493 bonds, 2 pseudobonds, 445 residues, 2 models selected
> color #1 #ef9a55ff
> select ::name="LIG"
60 atoms, 62 bonds, 1 residue, 1 model selected
> color sel light sea green
> color sel forest green
> select ::name="Y01"
252 atoms, 261 bonds, 3 residues, 1 model selected
> color sel light gray
> show #!2 models
> color zone #2 near #1 distance 4
> volume splitbyzone #2
Opened J277_aligned_topdb.mrc 0 as #3.1, grid size 256,256,256, pixel 0.727,
shown at level 0.0825, step 1, values float32
Opened J277_aligned_topdb.mrc 1 as #3.2, grid size 256,256,256, pixel 0.727,
shown at level 0.0825, step 1, values float32
Opened J277_aligned_topdb.mrc 2 as #3.3, grid size 256,256,256, pixel 0.727,
shown at level 0.0825, step 1, values float32
Opened J277_aligned_topdb.mrc 3 as #3.4, grid size 256,256,256, pixel 0.727,
shown at level 0.0825, step 1, values float32
> hide #!3.3 models
> hide #!3.2 models
> hide #!1 models
> volume #3.4 level 0.01319
> surface dust #3.1 size 7.27
> surface dust #3.4 size 7.27
> show #!1 models
> volume #3.1 level 0.1303
> select add #3.1
252 atoms, 261 bonds, 3 residues, 3 models selected
> select subtract #3.1
252 atoms, 261 bonds, 3 residues, 1 model selected
> select add #3.2
252 atoms, 261 bonds, 3 residues, 3 models selected
> show #!3.2 models
> show #!3.3 models
> select add #3.3
252 atoms, 261 bonds, 3 residues, 5 models selected
> select subtract #3.3
252 atoms, 261 bonds, 3 residues, 3 models selected
> volume #3.3 level 0.05619
> lighting gentle
> select clear
> surface dust #3.1 size 7.27
> surface dust #3.2 size 7.27
> surface dust #3.3 size 7.27
> surface dust #3.4 size 7.27
> ui tool show "Side View"
> view
> zoom
Pixel size at center of rotation is 0.163
> zoom 5
> view
> color #3.4 #42977eff models
> color #3.4 #086d97ff models
> color #3.4 #397497ff models
> color #3.4 #52a9dcff models
> color #3.4 #4c9bcbff models
> color #3.4 #89accbff models
> view name front
> view front
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/mariarafiq/Desktop/movie5.mp4
Movie saved to /Users/mariarafiq/Desktop/movie5.mp4
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> color #3.2 #ef9a557d models
> color #3.2 #ef9a5572 models
> hide #!1 models
> show #!1 models
> view front
> color #3.2 #ef9a55ff models
> hide #!3 models
> show #!2 models
> color #2 #ef9a55e6 models
> color #2 #ef9a55ff models
> hide #!1 models
> view front
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/mariarafiq/Desktop/movie6.mp4
Movie saved to /Users/mariarafiq/Desktop/movie6.mp4
> hide #!2 models
> show #!3 models
> show #!1 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/mariarafiq/Desktop/movie7.mp4
Movie saved to /Users/mariarafiq/Desktop/movie7.mp4
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!3.1 models
> hide #!3.2 models
> hide #!3.3 models
> color #3.4 #89accb86 models
Drag select of 13 residues
> select up
1922 atoms, 1949 bonds, 116 residues, 1 model selected
> select up
3598 atoms, 3652 bonds, 225 residues, 1 model selected
> select up
3702 atoms, 3755 bonds, 231 residues, 1 model selected
> select up
7071 atoms, 7170 bonds, 441 residues, 1 model selected
> hide sel atoms
> select clear
> hide #!3.4 models
Drag select of 1 atoms, 2 bonds
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> select up
60 atoms, 62 bonds, 1 residue, 1 model selected
> color sel #89accbff
> color sel byhetero
> select clear
> color byhetero
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> view front
> hide #!3 models
> show #!3.1 models
> show #!3.2 models
> show #!3.3 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> view front
> movie record
> turn y 2 180
> wait 180
> hide #!2 models
> show #!3 models
> show #!1 models
> turn y 2 180
> wait 180
> hide #!3.1 models
> hide #!3.2 models
> hide #!3.3 models
> turn y 2 180
> wait 180
> movie encode /Users/mariarafiq/Desktop/IXA4structure.mp4
Movie saved to /Users/mariarafiq/Desktop/IXA4structure.mp4
> hide #!3 models
> select /A:349
10 atoms, 9 bonds, 1 residue, 1 model selected
Drag select of 1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
60 atoms, 62 bonds, 1 residue, 1 model selected
> view sel
> show #!3 models
> volume #3.4 level 0.02985
> select add #1
7383 atoms, 7493 bonds, 2 pseudobonds, 445 residues, 2 models selected
> select subtract #1
Nothing selected
> select :LIG : select add :LIG
475 atoms, 467 bonds, 28 residues, 1 model selected
> show sel atoms
> hide H
> view
> select clear
> select :LIG : select clear
> save
> /Users/mariarafiq/Documents/SLC33/Ixa4/Phenix/deposition_Ixa4_SLC33/IXA4_zoomin_view.png
> width 2000 height 1408 supersample 4 transparentBackground true
> save /Users/mariarafiq/Downloads/IXA4_zoomin.png width 2000 height 1408
> supersample 4 transparentBackground true
> view name LIG
Drag select of 5 atoms, 10 residues, 3 bonds
> select up
849 atoms, 856 bonds, 55 residues, 1 model selected
> select up
6430 atoms, 6516 bonds, 401 residues, 1 model selected
> transparency 60
> transparency 90
> select clear
> undo
> view name LIG
> view LIG
> select clear
Drag select of 3.4 J277_aligned_topdb.mrc 3 , 4 atoms, 3 bonds
> select ~sel & ##selected
7379 atoms, 7490 bonds, 2 pseudobonds, 445 residues, 2 models selected
> select ~sel & ##selected
4 atoms, 3 bonds, 2 residues, 1 model selected
> select clear
Drag select of 3.4 J277_aligned_topdb.mrc 3 , 2 atoms, 1 bonds
> select ~sel & ##selected
7381 atoms, 7492 bonds, 2 pseudobonds, 445 residues, 2 models selected
> select clear
> view LIG
> save /Users/mariarafiq/Downloads/Session_IXA4_SLC.cxs includeMaps true
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/mariarafiq/Desktop/movie8.mp4
Movie saved to /Users/mariarafiq/Desktop/movie8.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/mariarafiq/Desktop/movie9.mp4
Movie saved to /Users/mariarafiq/Desktop/movie9.mp4
> hide #!1 models
> hide #!3 models
> hide #2.1 models
> hide #!3.4 models
> open
> /Users/mariarafiq/Documents/SLC33/Phenix/RealSpaceRefine_12/Refined12-coot-0.pdb
Chain information for Refined12-coot-0.pdb #4
---
Chain | Description
A | No description available
> view
> open
> /Users/mariarafiq/Documents/SLC33/Phenix/RealSpaceRefine_13/Refined12-coot-3_real_space_refined_013.pdb
Chain information for Refined12-coot-3_real_space_refined_013.pdb #5
---
Chain | Description
A | No description available
> open
> /Users/mariarafiq/Documents/SLC33/Phenix/RealSpaceRefine_10/Refine9_coot1.pdb
Chain information for Refine9_coot1.pdb #6
---
Chain | Description
A | No description available
> open
> /Users/mariarafiq/Documents/SLC33/Phenix/RealSpaceRefine_9/Refine7_coot1_real_space_refined_009.pdb
Chain information for Refine7_coot1_real_space_refined_009.pdb #7
---
Chain | Description
A | No description available
> open
> /Users/mariarafiq/Documents/SLC33/Phenix/RealSpaceRefine_8/Refine7_coot1-coot-0_real_space_refined_008.pdb
Chain information for Refine7_coot1-coot-0_real_space_refined_008.pdb #8
---
Chain | Description
A | No description available
> open
> /Users/mariarafiq/Documents/SLC33/Phenix/RealSpaceRefine_6/Refine_coot1_real_space_refined_006.pdb
Chain information for Refine_coot1_real_space_refined_006.pdb #9
---
Chain | Description
A | No description available
> close #9
> close #8
> close #7
> close #6
> close #5
> open
> "/Users/mariarafiq/Documents/SLC33/Phenix/Maps/cryosparc_P408_J557_003_volume_map_sharp
> (1).mrc"
Opened cryosparc_P408_J557_003_volume_map_sharp (1).mrc as #5, grid size
400,400,400, pixel 0.74, shown at level 0.0351, step 2, values float32
> volume #5 step 1
> volume #5 level 0.2563
> volume #5 level 0.2447
> surface dust #5 size 7.4
> volume #5 level 0.3029
> volume #5 level 0.1593
> surface dust #5 size 7.4
> open /Users/mariarafiq/Documents/SLC33/EMready_aligned_model.pdb
Chain information for EMready_aligned_model.pdb #6
---
Chain | Description
A | No description available
> close #6
> close #5
> close #4
> show #!1 models
> view
> show #!2 models
> select add #2
2 models selected
> show #2.1 models
> show #!3 models
> show #!3.1 models
> show #!3.2 models
> show #!3.3 models
> show #!3.4 models
> select subtract #2.1
1 model selected
> select add #2.1
2 models selected
> select subtract #2.1
1 model selected
> select add #2
2 models selected
> select subtract #2
Nothing selected
> open
> /Users/mariarafiq/Documents/SLC33/Ixa4/Phenix/deposition_Ixa4_SLC33/EMready.mrc
Opened EMready.mrc as #4, grid size 256,256,256, pixel 0.727, shown at level
0.545, step 1, values float32
> volume #4 level 5.832
> hide #!2 models
> hide #2.1 models
> hide #!3 models
> hide #!3.1 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> volume #4 level 3.432
> surface dust #4 size 7.27
> volume #4 level 4.373
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/mariarafiq/Downloads/emready2_map (17).mrc"
Opened emready2_map (17).mrc as #1, grid size 581,581,581, pixel 0.5, shown at
level -0.0245, step 4, values float32
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,1
Model Number: MW2V3LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 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: 3 days, 9 hours, 25 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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
LG FULL HD:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 8 weeks 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 , 8 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel says what we know about this crash:
"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 ChimeraX daily build uses a newer version of the Qt window toolkit (6.9.1 while your ChimeraX 1.10 uses 6.8.2) and we have not seen these multi-display Mac crashes in Qt 6.9.
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Reported by Maria Rafiq