Opened 9 months ago

Closed 9 months ago

#16974 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… 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-12.5-x86_64-i386-64bit
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 0x000000010b757600 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 59)


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{
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  "procLaunch" : "2025-02-26 15:54:48.5187 -0800",
  "procRole" : "Background",
  "version" : 2,
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  "captureTime" : "2025-02-26 16:17:29.3199 -0800",
  "incident" : "8FE1716C-B0DC-43EB-8B74-D5ED80F317AB",
  "bug_type" : "309",
  "pid" : 890,
  "procExitAbsTime" : 2737249523065,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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  "storeInfo" : {"deviceIdentifierForVendor":"505D6020-8AF6-5DA2-9609-064E2785D81E","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "C4744483-A6A2-441B-C31C-5761FB80AE6D",
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4408639488\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      106c68000-106c6c000    [   16K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "isCorpse" : 1,
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  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4408639488\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      106c68000-106c6c000    [   16K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
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    "base" : 140703467601920,
    "size" : 40960,
    "uuid" : "bd2bd848-f9c9-35ff-9795-32d31977523d",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5170298880,
    "size" : 183599104,
    "uuid" : "af091873-5278-3492-8e76-7c22e65c04ac",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703551197184,
    "CFBundleShortVersionString" : "1.600.0",
    "CFBundleIdentifier" : "com.apple.SkyLight",
    "size" : 3796992,
    "uuid" : "01618d26-b265-396b-bbea-d730ba46d7ff",
    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    "name" : "SkyLight"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703465717760,
    "size" : 290816,
    "uuid" : "5115c8ef-bc57-32db-91c6-71b61a79966e",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64h",
    "base" : 140703467819008,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5255168,
    "uuid" : "c39123bf-9d62-3577-a11f-0a97cc4d9991",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1866"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703615660032,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3096576,
    "uuid" : "95eab511-8fc1-353a-ac8a-26aa19032e2e",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703512354816,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15269888,
    "uuid" : "bcb46e9b-acd5-3b26-878f-a3988bc5df7e",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113.60.148"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4819664896,
    "size" : 655360,
    "uuid" : "a9df58b1-89b1-36c8-9d9e-fe251bf025f2",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4560367616,
    "size" : 5373952,
    "uuid" : "f4950342-54e3-3755-a88f-e2a6406c1fc3",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
    "name" : "QtCore"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4571586560,
    "size" : 2867200,
    "uuid" : "04d3e498-8e36-3f03-9aa5-8a19040cc57f",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
    "name" : "QtWidgets.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4408639488,
    "CFBundleShortVersionString" : "1.8.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
    "uuid" : "194a3167-3db5-3029-8d22-1d742b826bb9",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.8.0.0"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4486688768,
    "size" : 442368,
    "uuid" : "f71fb3ca-5fcc-3577-9457-b047888a46d1",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703466819584,
    "size" : 364544,
    "uuid" : "08aaa9d6-930c-3b45-a5ae-2905f436b834",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4580126720,
    "size" : 66404352,
    "uuid" : "7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  }
],
  "sharedCache" : {
  "base" : 140703464247296,
  "size" : 19331678208,
  "uuid" : "cc386fb1-8c26-3cb7-8329-cc63095fca7d"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 3792K        8 \nCG image                           104K        8 \nColorSync                          232K       27 \nCoreAnimation                      116K       12 \nCoreGraphics                        16K        3 \nCoreUI image data                 3464K       24 \nFoundation                          16K        1 \nIOKit                             15.5M        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             1.3G      491 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            256K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nObjC additional data                15K        1 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        144K       36 \nStack                            168.8M       38 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      276.1M      330 \nVM_ALLOCATE (reserved)            64.0M        1         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            51.8M      702 \n__DATA_CONST                      40.5M      396 \n__DATA_DIRTY                      1778K      228 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       677.5M      160 \n__TEXT                           852.4M      701 \n__UNICODE                          592K        1 \ndyld private memory               1056K        3 \nmapped file                      479.3M       54 \nshared memory                     3012K       31 \n===========                     =======  ======= \nTOTAL                              4.0G     3283 \nTOTAL, minus reserved VM space     3.9G     3283 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    },
    {
      "rolloutId" : "60186475825c62000ccf5450",
      "factorPackIds" : {

      },
      "deploymentId" : 240000083
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202404260133 (2024-04-26)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/rrajamanickam/Desktop/combo of trying things .pdb" format pdb

Summary of feedback from opening /Users/rrajamanickam/Desktop/combo of trying
things .pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 CYS B 738 ILE B 742 1 5  
Start residue of secondary structure not found: HELIX 2 2 THR B 747 LEU B 752
1 6  
Start residue of secondary structure not found: HELIX 3 3 LEU B 753 PHE B 759
1 7  
Start residue of secondary structure not found: HELIX 4 4 CYS B 760 PHE B 782
1 23  
Start residue of secondary structure not found: HELIX 5 5 PRO B 812 LYS B 814
1 3  
111 messages similar to the above omitted  
  
Chain information for combo of trying things .pdb  
---  
Chain | Description  
1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.8/F 1.8/H | No description available  
1.1/B 1.2/B 1.3/B 1.8/B 1.8/C 1.8/D | No description available  
1.5/B 1.6/B 1.7/B 1.8/E 1.8/G 1.8/I | No description available  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> open "/Users/rrajamanickam/Downloads/S2 structure 2/S2_mon.pdb"

Chain information for S2_mon.pdb #2  
---  
Chain | Description  
B | No description available  
  

> select add #2

3348 atoms, 3415 bonds, 1 pseudobond, 436 residues, 2 models selected  

> open "/Users/rrajamanickam/Downloads/S2 structure 2/S2_mon copy.pdb"

Chain information for S2_mon copy.pdb #3  
---  
Chain | Description  
B | No description available  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> select subtract #2

Nothing selected  

> open "/Users/rrajamanickam/Downloads/S2 structure 2/6C10_Fab copy.pdb"

Chain information for 6C10_Fab copy.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open "/Users/rrajamanickam/Downloads/S2 structure 2/S2_DS5_6C10_Fab.pdb"

Chain information for S2_DS5_6C10_Fab.pdb #5  
---  
Chain | Description  
A F H | No description available  
B C D | No description available  
E G I | No description available  
  

> show #4#!5 cartoons

> hide #4#!5 cartoons

> hide #4#!5 atoms

> show #4#!5 cartoons

> hide #4 models

> open "/Users/rrajamanickam/Downloads/S2 structure 2/enhanced.mrc"

Opened enhanced.mrc as #6, grid size 280,280,280, pixel 1.32, shown at level
3.8e-05, step 2, values float32  

> volume #6 level 0.1652

> hide #!5 models

> open "/Users/rrajamanickam/Downloads/S2 structure 2/S2_DS5_6C10_Fab.cxs"

Opened enhanced.mrc as #3, grid size 280,280,280, pixel 1.32, shown at level
0.279, step 1, values float32  
opened ChimeraX session  

> set bgColor white

> select add #2

5177 atoms, 5295 bonds, 1 pseudobond, 672 residues, 3 models selected  

> select subtract #9

3348 atoms, 3415 bonds, 1 pseudobond, 436 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.76075,-0.63479,0.13529,122.12,-0.64404,-0.71244,0.27863,419.72,-0.080488,-0.2991,-0.95082,511.7

> undo

> hide #8 models

> hide #7 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!3 models

> hide #9 models

> show #!2 models

> hide #!2 models

> select add #5

8525 atoms, 8710 bonds, 2 pseudobonds, 1108 residues, 5 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.57038,-0.80357,0.17015,191.7,-0.77338,-0.45561,0.4408,342.46,-0.27669,-0.38301,-0.88133,552.87,#5,-0.67653,0.73594,0.026556,167.06,-0.72475,-0.65898,-0.20121,470.14,-0.13058,-0.15537,0.97919,47.269,#9,-0.70218,0.71121,0.033571,174.25,-0.69966,-0.6805,-0.21772,471.82,-0.132,-0.17637,0.97543,57.309

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.57038,-0.80357,0.17015,191.79,-0.77338,-0.45561,0.4408,343.51,-0.27669,-0.38301,-0.88133,555.05,#5,-0.67653,0.73594,0.026556,167.16,-0.72475,-0.65898,-0.20121,471.19,-0.13058,-0.15537,0.97919,49.452,#9,-0.70218,0.71121,0.033571,174.34,-0.69966,-0.6805,-0.21772,472.86,-0.132,-0.17637,0.97543,59.492

> view matrix models
> #2,0.57038,-0.80357,0.17015,189.39,-0.77338,-0.45561,0.4408,345.85,-0.27669,-0.38301,-0.88133,551.85,#5,-0.67653,0.73594,0.026556,164.75,-0.72475,-0.65898,-0.20121,473.53,-0.13058,-0.15537,0.97919,46.254,#9,-0.70218,0.71121,0.033571,171.94,-0.69966,-0.6805,-0.21772,475.21,-0.132,-0.17637,0.97543,56.294

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.98383,-0.070892,0.16447,-67.382,-0.15816,-0.77479,0.61211,248.32,0.084035,-0.62823,-0.77348,506.39,#5,0.089306,0.96843,-0.23273,30.122,-0.9447,0.0083325,-0.32784,428.38,-0.31556,0.24913,0.91562,26.17,#9,0.056824,0.97476,-0.2159,29.75,-0.94205,-0.019267,-0.33493,432.2,-0.33064,0.22242,0.91717,38.022

> view matrix models
> #2,-0.016131,0.97406,0.2257,-125.53,0.91199,-0.078202,0.40268,-79.631,0.40989,0.21233,-0.88708,271.42,#5,0.82438,-0.24769,-0.50896,137.61,-0.0086944,0.89353,-0.44893,133.35,0.56597,0.37451,0.73445,-125.99,#9,0.83619,-0.21,-0.50664,125.94,-0.036938,0.90012,-0.43407,131.41,0.54719,0.38168,0.74492,-122.08

> view matrix models
> #2,-0.66092,-0.54793,0.51279,289.09,-0.58962,0.80185,0.096848,104.03,-0.46425,-0.23834,-0.85303,548.52,#5,-0.80933,-0.53029,-0.25254,441.32,0.58559,-0.76181,-0.277,260.76,-0.045498,-0.37207,0.92709,74.389,#9,-0.78835,-0.55401,-0.26755,443.46,0.61399,-0.73602,-0.2851,251.76,-0.038974,-0.38903,0.9204,82.727

> undo

> select add #5

8525 atoms, 8710 bonds, 2 pseudobonds, 1108 residues, 5 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.76075,-0.63479,0.13529,123.89,-0.64404,-0.71244,0.27863,418.68,-0.080488,-0.2991,-0.95082,513.05,#5,-0.46935,0.88294,-0.010917,113.27,-0.88295,-0.46913,0.017689,429.27,0.010497,0.017942,0.99978,-8.7914,#9,-0.50004,0.866,0.00014442,118.94,-0.866,-0.50004,0.0030834,434.73,0.0027425,0.0014168,1,0.86114

> view matrix models
> #2,0.76075,-0.63479,0.13529,123.36,-0.64404,-0.71244,0.27863,421.79,-0.080488,-0.2991,-0.95082,511.46,#5,-0.46935,0.88294,-0.010917,112.73,-0.88295,-0.46913,0.017689,432.38,0.010497,0.017942,0.99978,-10.379,#9,-0.50004,0.866,0.00014442,118.41,-0.866,-0.50004,0.0030834,437.84,0.0027425,0.0014168,1,-0.72677

> view matrix models
> #2,0.76075,-0.63479,0.13529,123.44,-0.64404,-0.71244,0.27863,421.49,-0.080488,-0.2991,-0.95082,511.25,#5,-0.46935,0.88294,-0.010917,112.82,-0.88295,-0.46913,0.017689,432.09,0.010497,0.017942,0.99978,-10.588,#9,-0.50004,0.866,0.00014442,118.5,-0.866,-0.50004,0.0030834,437.55,0.0027425,0.0014168,1,-0.93515

> view matrix models
> #2,0.76075,-0.63479,0.13529,123.4,-0.64404,-0.71244,0.27863,421.69,-0.080488,-0.2991,-0.95082,511.19,#5,-0.46935,0.88294,-0.010917,112.78,-0.88295,-0.46913,0.017689,432.29,0.010497,0.017942,0.99978,-10.643,#9,-0.50004,0.866,0.00014442,118.46,-0.866,-0.50004,0.0030834,437.75,0.0027425,0.0014168,1,-0.99021

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.74052,-0.64855,0.17608,119.74,-0.6691,-0.68712,0.28315,419.63,-0.062648,-0.3275,-0.94277,512.06,#5,-0.49936,0.86531,-0.043337,126.73,-0.86628,-0.4995,0.0082023,435.73,-0.014549,0.041638,0.99903,-9.7,#9,-0.52918,0.84788,-0.032795,132.27,-0.8482,-0.52964,-0.0067784,440.89,-0.023117,0.024229,0.99944,0.19228

> view matrix models
> #2,0.78153,-0.62168,0.052152,138.6,-0.61113,-0.7461,0.2643,426.78,-0.1254,-0.23843,-0.96303,509.4,#5,-0.42629,0.90248,0.061748,89.198,-0.90253,-0.42893,0.038219,425.91,0.060978,-0.039437,0.99736,-10.314,#9,-0.45822,0.8858,0.073454,95.312,-0.88712,-0.4609,0.024127,431.82,0.055227,-0.054107,0.99701,-1.2084

> view matrix models
> #2,0.7313,-0.68187,-0.015617,181.56,-0.656,-0.70945,0.25758,429.16,-0.18672,-0.17813,-0.96613,508.58,#5,-0.47084,0.86949,0.14931,87.727,-0.87598,-0.48086,0.037911,429.42,0.10476,-0.11294,0.98806,-4.9677,#9,-0.5022,0.8498,0.16011,94.932,-0.85876,-0.51185,0.023161,434.99,0.10163,-0.12586,0.98683,3.5317

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.7313,-0.68187,-0.015617,181.58,-0.656,-0.70945,0.25758,428.77,-0.18672,-0.17813,-0.96613,509.32,#5,-0.47084,0.86949,0.14931,87.744,-0.87598,-0.48086,0.037911,429.03,0.10476,-0.11294,0.98806,-4.2287,#9,-0.5022,0.8498,0.16011,94.949,-0.85876,-0.51185,0.023161,434.6,0.10163,-0.12586,0.98683,4.2707


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | QCoreApplication::postEvent: Unexpected null receiver  
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  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: 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: iMac
      Model Identifier: iMac19,2
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 16 GB
      System Firmware Version: 1731.140.1.0.0
      OS Loader Version: 540.120.3~19
      SMC Version (system): 2.47f3

Software:

    System Software Overview:

      System Version: macOS 12.5 (21G72)
      Kernel Version: Darwin 21.6.0
      Time since boot: 1:05

Graphics/Displays:

    Radeon Pro 560X:

      Chipset Model: Radeon Pro 560X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c2
      ROM Revision: 113-C981AA-042
      VBIOS Version: 113-C9819A1X-009
      EFI Driver Version: 01.B1.042
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 4096 x 2304 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP V22:
          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: CN40522NX3  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI


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 Eric Pettersen, 9 months ago

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

comment:2 by Tom Goddard, 9 months ago

Resolution: → duplicate
Status: assigned → closed
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