Crash on Mac waking from sleep

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.5-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202404260133 (2024-04-26 01:33:35 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x000000011452a600 (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.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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 59)


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{
  "uptime" : 2800,
  "procLaunch" : "2025-02-25 17:07:39.2926 -0800",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 1930725636,
  "deployVersion" : 210,
  "modelCode" : "iMac19,2",
  "procStartAbsTime" : 1695876997541,
  "coalitionID" : 609,
  "osVersion" : {
    "train" : "macOS 12.5",
    "build" : "21G72",
    "releaseType" : "User"
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  "captureTime" : "2025-02-25 17:26:36.8027 -0800",
  "incident" : "46CF71A1-3EFC-41EB-80AF-C968BBD741AA",
  "bug_type" : "309",
  "pid" : 931,
  "procExitAbsTime" : 2833344456063,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"8A5583BD-9771-5728-AADD-D57C081E9DCD","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: 4556230656\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10f929000-10f92d000    [   16K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4556230656\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10f929000-10f92d000    [   16K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
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  "faultingThread" : 0,
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    "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" : 140703324491776,
    "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" : 140703239012352,
    "size" : 290816,
    "uuid" : "5115c8ef-bc57-32db-91c6-71b61a79966e",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64h",
    "base" : 140703241113600,
    "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" : 140703388954624,
    "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" : 140703285649408,
    "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" : 4958040064,
    "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" : 4706263040,
    "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" : 4717481984,
    "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" : 4556230656,
    "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" : 4635402240,
    "size" : 442368,
    "uuid" : "f71fb3ca-5fcc-3577-9457-b047888a46d1",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703240114176,
    "size" : 364544,
    "uuid" : "08aaa9d6-930c-3b45-a5ae-2905f436b834",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4728840192,
    "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"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703385149440,
    "CFBundleShortVersionString" : "263.8",
    "CFBundleIdentifier" : "com.apple.Metal",
    "size" : 1314816,
    "uuid" : "9db34d77-f275-39bd-a0d6-2f03a1921547",
    "path" : "\/System\/Library\/Frameworks\/Metal.framework\/Versions\/A\/Metal",
    "name" : "Metal",
    "CFBundleVersion" : "263.8"
  }
],
  "sharedCache" : {
  "base" : 140703237541888,
  "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=4.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              2048K       16 \nActivity Tracing                   256K        1 \nCG backing stores                 3792K        8 \nCG image                          5372K       79 \nCG raster data                    3392K       20 \nColorSync                          232K       28 \nCoreAnimation                     34.0M      145 \nCoreGraphics                        16K        3 \nCoreServices                       140K        1 \nCoreUI image data                 7712K       72 \nFoundation                          32K        2 \nIOKit                             15.5M        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             3.6G      631 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            256K        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nObjC additional data                15K        1 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        152K       38 \nStack                            169.8M       39 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      388.8M      390 \nVM_ALLOCATE (reserved)            64.0M        1         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            51.9M      711 \n__DATA_CONST                      41.0M      406 \n__DATA_DIRTY                      1796K      233 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       677.5M      160 \n__TEXT                           856.0M      711 \n__UNICODE                          592K        1 \ndyld private memory               1056K        3 \nmapped file                      213.8M       55 \nshared memory                     3012K       33 \n===========                     =======  ======= \nTOTAL                              6.1G     3810 \nTOTAL, minus reserved VM space     6.1G     3810 \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/Downloads/S2 structure/S2_DS5_6C10_Fab.cxs"
> format session

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  

> open "/Users/rrajamanickam/Desktop/colored trimer plus fab .pdb"

Chain information for colored trimer plus fab .pdb #10  
---  
Chain | Description  
A F H | No description available  
B C D | No description available  
E G I | No description available  
  

> open "/Users/rrajamanickam/Desktop/agan we cry .pdb"

Chain information for agan we cry .pdb #11  
---  
Chain | Description  
A F H | No description available  
B C D | No description available  
E G I | No description available  
  

> open "/Users/rrajamanickam/Desktop/fittd trimer .pdb"

Chain information for fittd trimer .pdb #12  
---  
Chain | Description  
A F H | No description available  
B C D | No description available  
E G I | No description available  
  

> open "/Users/rrajamanickam/Desktop/model combo three fab.pdb"

Summary of feedback from opening /Users/rrajamanickam/Desktop/model combo
three fab.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  
227 messages similar to the above omitted  
  
Chain information for model combo three fab.pdb  
---  
Chain | Description  
13.4/A 13.5/A 13.6/A 13.7/A 13.8/A 13.12/A 13.13/A 13.14/A 13.15/A 13.16/A 13.8/F 13.16/F 13.8/H 13.16/H | No description available  
13.1/B 13.2/B 13.3/B 13.8/B 13.9/B 13.10/B 13.11/B 13.16/B 13.8/C 13.16/C 13.8/D 13.16/D | No description available  
13.5/B 13.6/B 13.7/B 13.13/B 13.14/B 13.15/B 13.8/E 13.16/E 13.8/G 13.16/G 13.8/I 13.16/I | No description available  
  

> open "/Users/rrajamanickam/Desktop/mapped on threee.pdb"

Summary of feedback from opening /Users/rrajamanickam/Desktop/mapped on
threee.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  
227 messages similar to the above omitted  
  
Chain information for mapped on threee.pdb  
---  
Chain | Description  
14.4/A 14.5/A 14.6/A 14.7/A 14.8/A 14.12/A 14.13/A 14.14/A 14.15/A 14.16/A 14.8/F 14.16/F 14.8/H 14.16/H | No description available  
14.1/B 14.2/B 14.3/B 14.8/B 14.9/B 14.10/B 14.11/B 14.16/B 14.8/C 14.16/C 14.8/D 14.16/D | No description available  
14.5/B 14.6/B 14.7/B 14.13/B 14.14/B 14.15/B 14.8/E 14.16/E 14.8/G 14.16/G 14.8/I 14.16/I | No description available  
  

> open "/Users/rrajamanickam/Desktop/lets do this .pdb"

Chain information for lets do this .pdb #15  
---  
Chain | Description  
A F H | No description available  
B C D | No description available  
E G I | No description available  
  

> ui tool show "Command Line Interface"

> close #15

> close #14

> close #13

> close #12

> close #11

> open "/Users/rrajamanickam/Desktop/xdssd dsdcsdc.pdb"

Chain information for xdssd dsdcsdc.pdb #11  
---  
Chain | Description  
A F H | No description available  
B C D | No description available  
E G I | No description available  
  

> volume #3 level 0.3324

> set bgColor white

> hide #!2 models

> hide #!3 models

> hide #!11 models

> hide #!10 models

> hide #9 models

> hide #8 models

> show #8 models

> show #9 models

> show #!10 models

> hide #!10 models

> show #!2 models

> select subtract #9

Nothing selected  

> select add #9

1829 atoms, 1880 bonds, 236 residues, 1 model selected  

> combine #2,4,5,7,8,9

Remapping chain ID 'B' in S2_mon copy.pdb #4 to 'C'  
Remapping chain ID 'B' in S2_mon copy 2.pdb #5 to 'D'  
Remapping chain ID 'B' in combination #7 to 'E'  
Remapping chain ID 'A' in 6C10_Fab copy.pdb #8 to 'F'  
Remapping chain ID 'B' in 6C10_Fab copy.pdb #8 to 'G'  
Remapping chain ID 'A' in 6C10_Fab copy 2.pdb #9 to 'H'  
Remapping chain ID 'B' in 6C10_Fab copy 2.pdb #9 to 'I'  

> hide #!12 models

> show #!12 models

> hide #9 models

> hide #8 models

> hide #7 models

> hide #!5 models

> hide #!4 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> ui mousemode right select

Drag select of 420 residues  
Drag select of 5 residues  

> ui mousemode right select

Drag select of 35 atoms, 27 bonds, 2016 residues, 1 pseudobonds  

> save /Users/rrajamanickam/Desktop/trimer.pdb models #12

> color #7/A medium blue

> color #8/A medium blue

> color #9/A medium blue

> color #9/B cornflower blue

> color #8/B cornflower blue

> color #7/B cornflower blue

> show #!11 models

> show #!10 models

> show #9 models

> show #8 models

> show #7 models

> show #6 models

> hide #6 models

> show #!4 models

> show #!5 models

> show #!2 models

> hide #!12 models

> show #7-9#!2,4-5,10-11 cartoons

> hide #7-9#!2,4-5,10-11 atoms

> color #7/B cornflower blue

> color #8/B cornflower blue

> color #9/B cornflower blue

> hide #!10 models

> select #4/B

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

> color (#!4 & sel) #75eee5ff

> color (#!4 & sel) #2af2e6ff

> color (#!4 & sel) #2af1e6ff

> color (#!4 & sel) #2af0e5ff

> color (#!4 & sel) #2aefe4ff

> color (#!4 & sel) #2aeee3ff

> color (#!4 & sel) #29ede2ff

> color (#!4 & sel) #29ebe0ff

> color (#!4 & sel) #29eadfff

> color (#!4 & sel) #29e8ddff

> color (#!4 & sel) #28e7dcff

> color (#!4 & sel) #28e6dcff

> color (#!4 & sel) #28e5daff

> color (#!4 & sel) #28e3d9ff

> color (#!4 & sel) #28e3d8ff

> color (#!4 & sel) #28e2d8ff

> color (#!4 & sel) #28e2d7ff

> color (#!4 & sel) #27e1d6ff

> color (#!4 & sel) #27e0d5ff

> color (#!4 & sel) #27dfd5ff

> color (#!4 & sel) #27dfd4ff

> color (#!4 & sel) #27ded4ff

> color (#!4 & sel) #27ded3ff

> select #5/B

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

> color (#!5 & sel) #ad637bff

> color (#!5 & sel) #b85e7cff

> color (#!5 & sel) #b95e7cff

> color (#!5 & sel) #b95f7dff

> color (#!5 & sel) #ba5f7dff

> color (#!5 & sel) #bb607eff

> color (#!5 & sel) #bc607fff

> color (#!5 & sel) #bd607fff

> color (#!5 & sel) #be6180ff

> color (#!5 & sel) #bf6180ff

> color (#!5 & sel) #c06281ff

> color (#!5 & sel) #c16282ff

> color (#!5 & sel) #c26382ff

> color (#!5 & sel) #c26383ff

> color (#!5 & sel) #c36383ff

> color (#!5 & sel) #c36483ff

> color (#!5 & sel) #c46484ff

> color (#!5 & sel) #c56585ff

> color (#!5 & sel) #c66585ff

> color (#!5 & sel) #c76585ff

> color (#!5 & sel) #c76586ff

> color (#!5 & sel) #c96687ff

> color (#!5 & sel) #ca6788ff

> color (#!5 & sel) #cb6888ff

> color (#!5 & sel) #cc6889ff

> color (#!5 & sel) #cd698aff

> color (#!5 & sel) #cc6889ff

> color (#!5 & sel) #cd688aff

> color (#!5 & sel) #cd698aff

> color (#!5 & sel) #ce698aff

> color (#!5 & sel) #ce698bff

> color (#!5 & sel) #cf6a8bff

> color (#!5 & sel) #d06a8cff

> color (#!5 & sel) #d16a8cff

> color (#!5 & sel) #d16b8cff

> color (#!5 & sel) #d26b8dff

> color (#!5 & sel) #d46c8fff

> color (#!5 & sel) #d56d8fff

> color (#!5 & sel) #d66d90ff

> color (#!5 & sel) #d76e91ff

> color (#!5 & sel) #d86e91ff

> color (#!5 & sel) #d86e92ff

> color (#!5 & sel) #d96f92ff

> color (#!5 & sel) #de7195ff

> color (#!5 & sel) #df7296ff

> color (#!5 & sel) #de7195ff

> color (#!5 & sel) #dd7195ff

> color (#!5 & sel) #dd7194ff

> color (#!5 & sel) #dc7094ff

> color (#!5 & sel) #db7093ff

> color (#!5 & sel) #da6f92ff

> color (#!5 & sel) #d96e92ff

> color (#!5 & sel) #d86e91ff

> color (#!5 & sel) #d96f92ff

> color (#!5 & sel) #da6f93ff

> color (#!5 & sel) #db7093ff

> color (#!5 & sel) #dc7094ff

> color (#!5 & sel) #df7196ff


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

Log:
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  




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 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
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: 48 minutes

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


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    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: 2.2.4
    ChimeraX-ColorActions: 1.0.4
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202404260133
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DiffPlot: 1.0
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 1.0.3
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.38
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    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: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.1
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10