Opened 2 years ago

Closed 2 years ago

#9463 closed defect (duplicate)

XMAS: crash in ~QGridLayout()

Reported by: chimerax-bug-report@… Owned by: Richard Scheltema
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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 0x000000020465b600 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
  "uptime" : 1600000,
  "procLaunch" : "2023-07-20 11:45:00.7833 +0200",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,4",
  "procStartAbsTime" : 33412251262818,
  "coalitionID" : 168239,
  "osVersion" : {
    "train" : "macOS 12.2.1",
    "build" : "21D62",
    "releaseType" : "User"
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  "captureTime" : "2023-07-26 11:32:02.8089 +0200",
  "incident" : "75667618-EF33-4DFF-8B18-9BB2D5055242",
  "bug_type" : "309",
  "pid" : 91902,
  "procExitAbsTime" : 39125812397540,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"F1C621B2-C7E5-561A-A374-FF6BE21194D8","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "A836F094-85ED-DC13-6682-15BB59D5CB5A",
  "wakeTime" : 7753,
  "sleepWakeUUID" : "937E04E8-AF0C-4C3E-A3A9-9CD12FD8420D",
  "sip" : "enabled",
  "vmRegionInfo" : "0x1490f3a00108 is not in any region.  Bytes after previous region: 22131758858505  Bytes before following region: 82940321070840\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x00001490f3a00108","rawCodes":[1,22612795195656],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00001490f3a00108"},
  "vmregioninfo" : "0x1490f3a00108 is not in any region.  Bytes after previous region: 22131758858505  Bytes before following region: 82940321070840\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
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  "faultingThread" : 0,
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    "size" : 49152,
    "uuid" : "ee564342-d8f2-396d-b642-40092cf34d82",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5306757120,
    "size" : 174571520,
    "uuid" : "473ca65c-6149-3bfa-a88b-95ac735bcd3b",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4605317120,
    "size" : 64028672,
    "uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  }
],
  "sharedCache" : {
  "base" : 140703563038720,
  "size" : 15218196480,
  "uuid" : "5c9ff5db-8827-329a-8a37-2483935a9ea1"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=4.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.3G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1152K        9 \nActivity Tracing                   256K        1 \nCG backing stores                 6512K        5 \nCG image                          1168K       90 \nColorSync                          244K       29 \nCoreAnimation                     4804K      242 \nCoreGraphics                       140K       34 \nCoreUI image data                 5272K       51 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             2.5G      363 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)         664.0M        9         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1696K      421 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               900K       90 \nRosetta Thread Context             900K       90 \nSTACK GUARD                         32K        8 \nStack                            165.1M       45 \nStack Guard                       56.2M       37 \nVM_ALLOCATE                      234.5M      457 \nVM_ALLOCATE (reserved)           224.1M       18         reserved VM address space (unallocated)\n__DATA                            49.8M      849 \n__DATA_CONST                      30.4M      346 \n__DATA_DIRTY                      1642K      219 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       746.6M      304 \n__OBJC_RO                         81.8M        1 \n__OBJC_RW                         3136K        2 \n__TEXT                           900.4M      827 \n__UNICODE                          588K        1 \ndyld private memory               1056K        3 \nmapped file                        5.4G     1578 \nshared memory                     3012K       24 \nunshared pmap                     9968K        7 \n===========                     =======  ======= \nTOTAL                             11.2G     6187 \nTOTAL, minus reserved VM space    10.2G     6187 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "601d9415f79519000ccd4b69",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
      },
      "deploymentId" : 240000416
    },
    {
      "rolloutId" : "60356660bbe37970735c5624",
      "factorPackIds" : {

      },
      "deploymentId" : 240000027
    },
    {
      "rolloutId" : "602ad4dac86151000cf27e46",
      "factorPackIds" : {
        "SIRI_DICTATION_ASSETS" : "61fb0e87c773c43cde3bb80e"
      },
      "deploymentId" : 240000305
    },
    {
      "rolloutId" : "60da5e84ab0ca017dace9abf",
      "factorPackIds" : {

      },
      "deploymentId" : 240000008
    },
    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
      },
      "deploymentId" : 240000066
    },
    {
      "rolloutId" : "63582c5f8a53461413999550",
      "factorPackIds" : {

      },
      "deploymentId" : 240000002
    },
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    },
    {
      "rolloutId" : "5f72dc58705eff005a46b3a9",
      "factorPackIds" : {

      },
      "deploymentId" : 240000015
    },
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

      },
      "deploymentId" : 240000025
    },
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000614
    },
    {
      "rolloutId" : "60186475825c62000ccf5450",
      "factorPackIds" : {

      },
      "deploymentId" : 240000055
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000299
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/carolin/Desktop/20230413.cxs

Opened cryosparc_P170_J106_002_volume_map_sharp.mrc as #1, grid size
240,240,240, pixel 1.88, shown at level 0.591, step 1, values float32  
Opened emd_23033.map as #6, grid size 266,266,266, pixel 1.35, shown at level
0.0342, step 2, values float32  
Opened cryosparc_P198_J65_002_volume_map.mrc as #7, grid size 256,256,256,
pixel 1.88, shown at level 0.255, step 1, values float32  
Opened emd_22262.map gaussian as #13, grid size 320,320,320, pixel 0.9, shown
at level 0.281, step 1, values float32  
Opened emd_22263(1).map gaussian as #14, grid size 256,256,256, pixel 1.19,
shown at level 0.245, step 1, values float32  
Opened emd_22264(2).map gaussian as #15, grid size 256,256,256, pixel 1.19,
shown at level 0.172, step 1, values float32  
Opened emd_22260(1).map gaussian as #17, grid size 256,256,256, pixel 1.14,
shown at level 0.355, step 1, values float32  
Opened emd_22261.map gaussian as #12, grid size 256,256,256, pixel 1.19, shown
at level 0.248, step 1, values float32  
opened ChimeraX session  

> show #2 models

> show #!3 models

> show #4 models

> hide #!15 models

> ui tool show XMAS

  
Peptide pair mapping of XlinkX evidence file:
/Users/carolin/Library/CloudStorage/OneDrive-
TUM/PhD/MS/202305_spf1EMCPhoX/20230531_EXPL6_BaSt_SA_LC12_16_07_Orbi4683_Sample01-(1)_Crosslinks.txt  
Unique peptide pairs: 292 out of 292  
Unique peptide pairs with pseudobonds: 270  
Pseudobonds are stored in /Users/carolin/Library/CloudStorage/OneDrive-
TUM/PhD/MS/202305_spf1EMCPhoX/20230531_EXPL6_BaSt_SA_LC12_16_07_Orbi4683_Sample01-(1)_Crosslinks_2,3,4.pb  
Mapping information is stored in /Users/carolin/Library/CloudStorage/OneDrive-
TUM/PhD/MS/202305_spf1EMCPhoX/20230531_EXPL6_BaSt_SA_LC12_16_07_Orbi4683_Sample01-(1)_Crosslinks_2,3,4.tsv  

> select subtract #5

Nothing selected  

> hide #4 models

> hide #!3 models

> show #4 models

> hide #!7 models

> show #!1 models

> color #1 #2f4f4f8e models

> color #1 #598f918e models

> color #1 #598f918f models

> hide #!1 models

> show #!7 models

> fint #4 in #7

Unknown command: fint #4 in #7  

> fitmap #4 inMap #7

Fit molecule AF-P39986-F1-model_v4.pdb (#4) to map
cryosparc_P198_J65_002_volume_map.mrc (#7) using 9529 atoms  
average map value = 0.3418, steps = 208  
shifted from previous position = 19.7  
rotated from previous position = 37.7 degrees  
atoms outside contour = 2462, contour level = 0.25501  
  
Position of AF-P39986-F1-model_v4.pdb (#4) relative to
cryosparc_P198_J65_002_volume_map.mrc (#7) coordinates:  
Matrix rotation and translation  
0.38082595 0.88270423 0.27532679 241.17345708  
0.37366671 -0.41928482 0.82738953 173.11347438  
0.84578058 -0.21221095 -0.48951173 236.92766700  
Axis -0.80560001 -0.44205210 -0.39445983  
Axis point 0.00000000 41.55488813 56.67509134  
Rotation angle (degrees) 139.81680369  
Shift along axis -364.27296296  
  

> ui tool show "Volume Viewer"

> volume #7 level 0.3144

> select #1:963:966:967:970:974

Nothing selected  

> fitmap #4 inMap #7

Fit molecule AF-P39986-F1-model_v4.pdb (#4) to map
cryosparc_P198_J65_002_volume_map.mrc (#7) using 9529 atoms  
average map value = 0.3418, steps = 48  
shifted from previous position = 0.0245  
rotated from previous position = 0.133 degrees  
atoms outside contour = 4125, contour level = 0.31443  
  
Position of AF-P39986-F1-model_v4.pdb (#4) relative to
cryosparc_P198_J65_002_volume_map.mrc (#7) coordinates:  
Matrix rotation and translation  
0.38254078 0.88163328 0.27637892 241.18892888  
0.37331665 -0.42111456 0.82661793 173.13725664  
0.84516107 -0.21303821 -0.49022188 236.92817498  
Axis -0.80625390 -0.44109086 -0.39419982  
Axis point 0.00000000 41.74763916 56.67382879  
Rotation angle (degrees) 139.85344998  
Shift along axis -364.22582063  
  

> matchmaker #4 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xmp, chain A (#3) with AF-P39986-F1-model_v4.pdb, chain A (#4),
sequence alignment score = 5792.6  
RMSD between 431 pruned atom pairs is 1.172 angstroms; (across all 1086 pairs:
4.183)  
  

> show #!3 models

> show #!1 models

> volume #1 level 0.2565

> hide #!7 models

> volume #1 level 0.1335

> fitmap #3 inMap #1

Fit molecule 6xmp (#3) to map cryosparc_P170_J106_002_volume_map_sharp.mrc
(#1) using 8865 atoms  
average map value = 0.4132, steps = 128  
shifted from previous position = 17.1  
rotated from previous position = 12.2 degrees  
atoms outside contour = 312, contour level = 0.13353  
  
Position of 6xmp (#3) relative to cryosparc_P170_J106_002_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.82288376 -0.42301473 0.37936902 122.91123690  
-0.55180064 -0.75421385 0.35591786 306.58992594  
0.13556688 -0.50221509 -0.85405013 390.03251791  
Axis -0.95206139 0.27048794 -0.14288239  
Axis point 0.00000000 217.92386601 144.41590023  
Rotation angle (degrees) 153.21325639  
Shift along axis -89.81894348  
  

> fitmap #3 inMap #1

Fit molecule 6xmp (#3) to map cryosparc_P170_J106_002_volume_map_sharp.mrc
(#1) using 8865 atoms  
average map value = 0.4132, steps = 60  
shifted from previous position = 0.0332  
rotated from previous position = 0.00979 degrees  
atoms outside contour = 312, contour level = 0.13353  
  
Position of 6xmp (#3) relative to cryosparc_P170_J106_002_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.82294592 -0.42289056 0.37937263 122.89182579  
-0.55170990 -0.75421742 0.35605094 306.55270066  
0.13555886 -0.50231430 -0.85399306 390.07218729  
Axis -0.95207714 0.27043210 -0.14288317  
Axis point 0.00000000 217.91590869 144.43091939  
Rotation angle (degrees) 153.20590486  
Shift along axis -89.83555746  
  

> fitmap #4 inMap #1

Fit molecule AF-P39986-F1-model_v4.pdb (#4) to map
cryosparc_P170_J106_002_volume_map_sharp.mrc (#1) using 9529 atoms  
average map value = 0.4586, steps = 312  
shifted from previous position = 29.1  
rotated from previous position = 66.6 degrees  
atoms outside contour = 234, contour level = 0.13353  
  
Position of AF-P39986-F1-model_v4.pdb (#4) relative to
cryosparc_P170_J106_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.37073789 0.91047960 -0.18324932 227.81659596  
0.41997681 0.01163141 0.90746030 169.96081304  
0.82835554 -0.41339038 -0.37806811 220.81243315  
Axis -0.76150483 -0.58321655 -0.28278764  
Axis point 0.00000000 45.66716890 77.77986118  
Rotation angle (degrees) 119.85781960  
Shift along axis -335.05042392  
  

> matchmaker #4 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xmp, chain A (#3) with AF-P39986-F1-model_v4.pdb, chain A (#4),
sequence alignment score = 5792.6  
RMSD between 431 pruned atom pairs is 1.172 angstroms; (across all 1086 pairs:
4.183)  
  

> select subtract #5

Nothing selected  

> hide #!3 models

> show #!7 models

> hide #!1 models

> volume #7 level 0.2245

> hide #!7 models

> show #!12 models

> hide #!12 models

> show #!6 models

> hide #!6 models

> show #!13 models

> hide #!13 models

> show #!14 models

> hide #!14 models

> show #!17 models

> hide #!17 models

> show #!15 models

> show #!1 models

> show #!7 models

> hide #!1 models

> hide #!7 models

> hide #!15 models

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/carolin/Desktop/movie1.mp4

Movie saved to /Users/carolin/Desktop/movie1.mp4  
  

> select add #2

34122 atoms, 34491 bonds, 141 pseudobonds, 2124 residues, 2 models selected  

> show target m

> select add #5

34122 atoms, 34491 bonds, 531 pseudobonds, 2124 residues, 2 models selected  

> select subtract #5

34122 atoms, 34491 bonds, 2124 residues, 1 model selected  

> hide #!1 models

> hide #!3 models

> hide #!6 models

> hide #!7 models

> hide #8 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!17 models

> view #17 clip false

No displayed objects specified.  

> view #2 clip false

> select subtract #5

34122 atoms, 34491 bonds, 2124 residues, 1 model selected  

> select add #5

34122 atoms, 34491 bonds, 531 pseudobonds, 2124 residues, 2 models selected  

> select subtract #2

346 pseudobonds, 1 model selected  

> select add #5

531 pseudobonds, 1 model selected  

> select subtract #5

Nothing selected  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/carolin/Desktop/movie2.mp4

Movie saved to /Users/carolin/Desktop/movie2.mp4  
  

> ui tool show "Side View"

> select #4/d

Nothing selected  

> select #2/d

3029 atoms, 3066 bonds, 9 pseudobonds, 190 residues, 2 models selected  

> select add #4

12558 atoms, 12806 bonds, 113 pseudobonds, 1405 residues, 3 models selected  

> select clear

> select add #4

9529 atoms, 9740 bonds, 104 pseudobonds, 1215 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.759,0.64388,-0.096636,250.56,0.14171,0.30822,0.9407,114.79,0.63548,0.7003,-0.32518,208.73,#5,1,0,0,0,0,1,0,0,0,0,1,0

> select subtract #4

Nothing selected  

> ui mousemode right translate

> sel#4:838-952

Unknown command: sel#4:838-952  

> select #4/A:838-952

889 atoms, 910 bonds, 12 pseudobonds, 115 residues, 2 models selected  

> color (#4 & sel) hot pink

> select clear


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

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,4
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 32 GB

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 55 days 20:03

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        PHL 346B1C:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 100.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    et-xmlfile: 1.1.0
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openpyxl: 3.1.2
    openvr: 1.23.701
    packaging: 21.3
    pandas: 2.0.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    seaborn: 0.12.2
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Third Party
Owner: set to Richard Scheltema
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → XMAS: crash in ~QGridLayout()

comment:2 by Eric Pettersen, 2 years ago

Resolution: → duplicate
Status: assigned → closed

The fix for this problem is sitting in a pull request on the XMAS GitHub repository.

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