Opened 3 months ago

Closed 3 months ago

#18209 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: minhducdkh@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-15.5-x86_64-i386-64bit
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 0x00007ff858663dc0 (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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, 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, PIL._imaging, PIL._imagingmath, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 51)


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  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,1",
  "coalitionID" : 10277,
  "osVersion" : {
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  "captureTime" : "2025-07-16 14:45:46.4256 +0200",
  "codeSigningMonitor" : 0,
  "incident" : "2D9D0431-EA03-48D3-9B3F-D2D6C16D10C7",
  "pid" : 57931,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-07-11 19:28:26.7883 +0200",
  "procStartAbsTime" : 26802715046332,
  "procExitAbsTime" : 243484592994489,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
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  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "5A8EFE95-C9B8-50CB-3111-3AE68D059CBA",
  "appleIntelligenceStatus" : {"reasons":["deviceNotCapable"],"state":"unavailable"},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "bootSessionUUID" : "307A6ACD-CC28-48CD-9F2C-F0D24696DF61",
  "wakeTime" : 10894,
  "bridgeVersion" : {"build":"22P5072","train":"9.5"},
  "sleepWakeUUID" : "0EBDBC43-D5BB-4AFF-958D-7DBBCCF64647",
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4515893248\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10d2b1000-10d2b5000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":57931},
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4515893248\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10d2b1000-10d2b5000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
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QDeadlineTimer)","symbolLocation":84,"imageIndex":45},{"imageOffset":5265794,"symbol":"QFileInfoGatherer::run()","symbolLocation":178,"imageIndex":50},{"imageOffset":2324203,"imageIndex":45},{"imageOffset":24049,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":140},{"imageOffset":6231,"symbol":"thread_start","symbolLocation":15,"imageIndex":140}]},{"id":9625957,"frames":[{"imageOffset":6196,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":140}],"threadState":{"r13":{"value":0},"rax":{"value":33554800},"rflags":{"value":512},"cpu":{"value":0},"r14":{"value":1},"rsi":{"value":258063},"r8":{"value":409604},"cr2":{"value":0},"rdx":{"value":123145493471232},"r10":{"value":0},"r9":{"value":18446744073709551615},"r15":{"value":123145493994360},"rbx":{"value":123145493995520},"trap":{"value":133},"err":{"value":33554800},"r11":{"value":582},"rip":{"value":140703510665268},"rbp":{"value":0},"rsp":{"value":123145493995520},"r12":{"value":5193734},"rcx":{"value":0},"flavor":"x86_THREAD_STATE","rdi":{"value":123145493995520}}},{"id":9636378,"frames":[{"imageOffset":6196,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":140}],"threadState":{"r13":{"value":0},"rax":{"value":33554800},"rflags":{"value":512},"cpu":{"value":0},"r14":{"value":1},"rsi":{"value":233503},"r8":{"value":409602},"cr2":{"value":0},"rdx":{"value":123145654161408},"r10":{"value":0},"r9":{"value":18446744073709551615},"r15":{"value":123145654684536},"rbx":{"value":123145654685696},"trap":{"value":133},"err":{"value":33554800},"r11":{"value":582},"rip":{"value":140703510665268},"rbp":{"value":0},"rsp":{"value":123145654685696},"r12":{"value":5193730},"rcx":{"value":0},"flavor":"x86_THREAD_STATE","rdi":{"value":123145654685696}}},{"id":9636964,"frames":[{"imageOffset":6196,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":140}],"threadState":{"r13":{"value":0},"rax":{"value":33554800},"rflags":{"value":512},"cpu":{"value":0},"r14":{"value":0},"rsi":{"value":109215},"r8":{"value":409604},"cr2":{"value":0},"rdx":{"value":123145654697984},"r10":{"value":0},"r9":{"value":18446744073709551615},"r15":{"value":0},"rbx":{"value":123145655222272},"trap":{"value":133},"err":{"value":33554800},"r11":{"value":582},"rip":{"value":140703510665268},"rbp":{"value":0},"rsp":{"value":123145655222272},"r12":{"value":0},"rcx":{"value":0},"flavor":"x86_THREAD_STATE","rdi":{"value":123145655222272}}}],
  "usedImages" : [
[deleted to fit within ticket limits]

],
  "sharedCache" : {
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  "size" : 30064771072,
  "uuid" : "57b0c2b8-36d6-3cf0-8bd0-0ac6133ec8b3"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=13.3G written=375.8M(3%) resident=0K(0%) swapped_out=375.8M(3%) unallocated=12.9G(97%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 9276K        1 \nCG image                           592K       44 \nCG raster data                     100K        8 \nColorSync                          264K       33 \nCoreAnimation                      976K      107 \nCoreGraphics                        16K        3 \nCoreUI image data                 5208K       43 \nFoundation                          36K        2 \nIOKit                             23.3M        3 \nKernel Alloc Once                    8K        1 \nMALLOC                            12.3G     2988 \nMALLOC guard page                   48K       12 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        156K       39 \nStack                            192.8M       40 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      624.6M      538 \nVM_ALLOCATE (reserved)           128.0M        2         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            45.0M     1095 \n__DATA_CONST                     123.4M     1036 \n__DATA_DIRTY                      2590K      343 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       192.0M      141 \n__OBJC_RO                         61.3M        1 \n__OBJC_RW                         2395K        2 \n__TEXT                             1.4G     1114 \n__TPRO_CONST                         16        2 \ndyld private memory               1608K       14 \nmapped file                      561.7M       84 \nshared memory                     3548K       37 \n===========                     =======  ======= \nTOTAL                             15.7G     7748 \nTOTAL, minus reserved VM space    15.6G     7748 \n",
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  "logWritingSignature" : "b502cdb94368407f9118fa5f15a9a4a3ff8e9234",
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}
===== 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/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/map_for_refinement/final map for
> figures/cryosparc_P9_J711_HIGD2A.mrc"

Opened cryosparc_P9_J711_HIGD2A.mrc as #1, grid size 600,600,600, pixel 0.84,
shown at level 0.102, step 4, values float32  

> volume #1 level 0.2413

> open "/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/map_for_refinement/final map for
> figures/cryosparc_P9_J716_map_locres-class1-complexIV.mrc"

Opened cryosparc_P9_J716_map_locres-class1-complexIV.mrc as #2, grid size
600,600,600, pixel 0.84, shown at level 0.00241, step 4, values float32  

> volume #1 level 0.2878

> ui tool show "Surface Color"

> color sample #1.1 map #2 palette
> 2.5,#0000ff:3.5,#00aaff:4.5,#00ffa9:5.5,#00ff00:6.5,#aaff00:7.5,#ffaa00:40,#ff0000
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 3.889, maximum 42.89  

> hide #!2 models

[deleted to fit within ticket limits]


Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> select #4/B:60

15 atoms, 14 bonds, 1 residue, 1 model selected  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> select up

64 atoms, 63 bonds, 4 residues, 1 model selected  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> select up

3539 atoms, 3584 bonds, 222 residues, 1 model selected  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(NoModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> color bfactor sel key true

> key blue-white-red :59 :109 :159 showTool true

3539 atoms, 222 residues, atom bfactor range 59.3 to 159  

> show #3 models

> select clear

> save "/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/C14_supercomplex_project/HIGD2A-Manuscript/revise/figure
> revise/B factor cox 2 NDUFA4 bound.png" width 1500 height 1387 supersample 3
> transparentBackground true

> hide #3 models

> select #4/B:62

15 atoms, 14 bonds, 1 residue, 1 model selected  

> hide #!4 models

> select add #4

30740 atoms, 31201 bonds, 26 pseudobonds, 1862 residues, 2 models selected  

> select subtract #4

Nothing selected  

> show #!1 models

> ui tool show "Surface Color"

> color sample #1.1 map #2 palette
> 2.5,#0000ff:3.5,#00aaff:4.5,#00ffa9:5.5,#00ff00:6.5,#aaff00:7.5,#ffaa00:30,#ff0000
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 3.865, maximum 43.55  
Map values for surface "cap far": minimum 2.706, mean 3.656, maximum 7.562  

> color sample #1.1 map #2 palette
> 2.5,#0000ff:3.5,#00aaff:4.5,#00ffa9:5.5,#00ff00:6.5,#aaff00:7.5,#ffaa00:30,#ff0000
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 3.865, maximum 43.55  
Map values for surface "cap far": minimum 2.706, mean 3.656, maximum 7.562  

> show #!11 models

> hide #!1 models

> volume #11 level 0.3441

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!11 models

> show #!1 models

> volume #1 level 0.3278

> show #!14 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!4,14 cartoons

> select add #4

30740 atoms, 31201 bonds, 26 pseudobonds, 1862 residues, 2 models selected  

> show sel cartoons

> select subtract #4

Nothing selected  

> select add #14

30444 atoms, 30892 bonds, 23 pseudobonds, 1849 residues, 2 models selected  

> show sel cartoons

> select subtract #14

14 models selected  

> select ::name="PGV"

432 atoms, 428 bonds, 4 residues, 4 models selected  

> show sel & #!4,14 atoms

> select add #13

30785 atoms, 31220 bonds, 19 pseudobonds, 1852 residues, 5 models selected  

> select subtract #13

305 atoms, 302 bonds, 3 residues, 17 models selected  

> hide #!1 models

> show #!1 models

> hide sel & #!4,14 atoms

> select add #4

30918 atoms, 31377 bonds, 26 pseudobonds, 1864 residues, 4 models selected  

> select subtract #4

178 atoms, 176 bonds, 2 residues, 2 models selected  

> select add #5

15280 atoms, 15721 bonds, 7 pseudobonds, 1850 residues, 4 models selected  

> select subtract #5

127 atoms, 126 bonds, 1 residue, 3 models selected  

> hide #!4 models

> hide #!1 models

> show #!11 models

> select add #14

30444 atoms, 30892 bonds, 23 pseudobonds, 1849 residues, 2 models selected  

> select subtract #14

14 models selected  

> hide #!14 models

> show #!4 models

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(NoModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> volume #11 level 0.3

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(NoModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> volume #11 level 0.28

> select #4/B:62@CD

1 atom, 1 residue, 1 model selected  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(NoModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> volume zone #11 nearAtoms sel range 5 newMap true

Opened cryosparc_P9_J715_NDUFA4.mrc zone as #15, grid size 600,600,600, pixel
0.84, shown at step 1, values float32  

> volume #15 level 0.2653

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(NoModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> volume zone #11 nearAtoms sel range 3.5 newMap true

Opened cryosparc_P9_J715_NDUFA4.mrc zone as #16, grid size 600,600,600, pixel
0.84, shown at step 1, values float32  

> hide #!15 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!14 models


===== 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  




OpenGL version: 4.1 ATI-7.0.3
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0)
      OS Loader Version: 583~1350

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 5 days, 11 hours, 9 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL P2319H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: B7HMY43     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version:  2.4a


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 (3)

comment:1 by Eric Pettersen, 3 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

Reported by Duc Nguyen

comment:2 by Tom Goddard, 3 months ago

The ChimeraX bug report panel explained 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."

We thought the ChimeraX 1.10 fixed it, but apparently not. You are the second person to report this Qt Mac multi-display crash in ChimeraX 1.10. Do you recall what you were doing when it crashed? Were you plugging in or unplugging an external display? Did you have more than one display connected? Were you dragging a window between displays? Did you just wake the computer from sleep? These are all cases that triggered the Qt bug in ChimeraX 1.9 and I'd like to know how it can be triggered in ChimeraX 1.10.

comment:3 by Tom Goddard, 3 months ago

Resolution: → duplicate
Status: assigned → closed

No response from reporter.

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