Opened 3 years ago

Closed 3 years ago

#8681 closed defect (duplicate)

Crash in garbage collection

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: UI Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.2.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 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 0x00000001022a8580 (most recent call first):
  File "/private/var/folders/fj/pm6yj9d1445f7x9pkjp8rhrc0000gn/T/AppTranslocation/4E446B59-C515-4F45-AA83-A934E3CA1221/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 341 in _cleanup
  File "/private/var/folders/fj/pm6yj9d1445f7x9pkjp8rhrc0000gn/T/AppTranslocation/4E446B59-C515-4F45-AA83-A934E3CA1221/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 381 in cb
  File "/private/var/folders/fj/pm6yj9d1445f7x9pkjp8rhrc0000gn/T/AppTranslocation/4E446B59-C515-4F45-AA83-A934E3CA1221/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/private/var/folders/fj/pm6yj9d1445f7x9pkjp8rhrc0000gn/T/AppTranslocation/4E446B59-C515-4F45-AA83-A934E3CA1221/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/private/var/folders/fj/pm6yj9d1445f7x9pkjp8rhrc0000gn/T/AppTranslocation/4E446B59-C515-4F45-AA83-A934E3CA1221/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/private/var/folders/fj/pm6yj9d1445f7x9pkjp8rhrc0000gn/T/AppTranslocation/4E446B59-C515-4F45-AA83-A934E3CA1221/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/fj/pm6yj9d1445f7x9pkjp8rhrc0000gn/T/AppTranslocation/4E446B59-C515-4F45-AA83-A934E3CA1221/d/ChimeraX-1.5.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" : 170000,
  "procLaunch" : "2023-03-20 11:00:59.7687 -0400",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro17,1",
  "procStartAbsTime" : 4117909740491,
  "coalitionID" : 22622,
  "osVersion" : {
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    "build" : "21D62",
    "releaseType" : "User"
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  "captureTime" : "2023-03-20 11:40:53.9423 -0400",
  "incident" : "449AED55-C728-41B7-9B5E-C0BD50511B5E",
  "bug_type" : "309",
  "pid" : 59904,
  "procExitAbsTime" : 4175367924912,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"BB86D291-B782-5496-9264-F9768E95C42D","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "6CAFF911-3FFC-788C-E9D6-DA4F0B1A4804",
  "wakeTime" : 2485,
  "sleepWakeUUID" : "DBFB17C3-0B97-4F52-8A46-411D17048FC3",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 4330241879\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1021a4000-1021a8000    [   16K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "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" : "0xa9 is not in any region.  Bytes before following region: 4330241879\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1021a4000-1021a8000    [   16K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
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  "faultingThread" : 0,
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    "size" : 20709376,
    "uuid" : "6b8373ed-7142-34ea-9b4b-9f502e8a6f33",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5832228864,
    "size" : 144654336,
    "uuid" : "21c8f378-4426-330a-89d1-26ab67c6fa56",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  }
],
  "sharedCache" : {
  "base" : 6639910912,
  "size" : 3091218432,
  "uuid" : "296eb28e-6aeb-3129-8fa6-feb92261a4eb"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=2.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.1G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1536K       12 \nActivity Tracing                   256K        1 \nCG backing stores                 2176K        4 \nCG image                           896K       26 \nColorSync                          640K       28 \nCoreAnimation                     2688K       22 \nCoreGraphics                        32K        2 \nCoreUI image data                 1840K       12 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                           747.9M      126 \nMALLOC guard page                  192K       10 \nMALLOC_MEDIUM (reserved)         760.0M        7         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        544K       34 \nStack                            153.3M       35 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      239.6M      546 \nVM_ALLOCATE (reserved)           160.0M        1         reserved VM address space (unallocated)\n__AUTH                            2582K      311 \n__AUTH_CONST                      19.8M      502 \n__DATA                            22.6M      623 \n__DATA_CONST                      26.7M      635 \n__DATA_DIRTY                      1787K      215 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       603.3M      132 \n__OBJC_CONST                      3589K      276 \n__OBJC_RO                         82.1M        1 \n__OBJC_RW                         3104K        1 \n__TEXT                           690.5M      653 \n__UNICODE                          588K        1 \ndyld private memory               1184K        3 \nmapped file                      189.2M       50 \nshared memory                     3184K       23 \n===========                     =======  ======= \nTOTAL                              3.8G     4306 \nTOTAL, minus reserved VM space     2.8G     4306 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "601d9415f79519000ccd4b69",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
      },
      "deploymentId" : 240000416
    },
    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
      },
      "deploymentId" : 240000066
    },
    {
      "rolloutId" : "60356660bbe37970735c5624",
      "factorPackIds" : {

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

      },
      "deploymentId" : 240000008
    },
    {
      "rolloutId" : "60186475825c62000ccf5450",
      "factorPackIds" : {

      },
      "deploymentId" : 240000026
    },
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      "rolloutId" : "63582c5f8a53461413999550",
      "factorPackIds" : {

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

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

      },
      "deploymentId" : 240000015
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000251
    },
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

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

      },
      "deploymentId" : 240000612
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/joannavuille/Library/CloudStorage/OneDrive-
> PartnersHealthCare/Joanna/Projects/HECTD4/Alphafold prediction/2.
> Juan_test2_forJoanna_HECTD4/prediction_1_HECTD4(0001-1499)_cEPHA2/best_model.pdb"

Chain information for best_model.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> color bychain

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "/Users/joannavuille/Library/CloudStorage/OneDrive-
> PartnersHealthCare/Joanna/Projects/HECTD4/Alphafold prediction/2.
> Juan_test2_forJoanna_HECTD4/prediction_1_HECTD4(0001-1499)_cEPHA2/best_model_pae.json"

> color #1/B:4-1246 lime

> color #1/B:1349-1349 lime

> color #1/B:1001-1001 magenta

> alphafold pae #1 colorDomains true

> color #1/B:352-352 lime

> color #1/B:333-333 magenta

> color #1/B:369-369 lime

> color #1/B:685-685 magenta

> color #1/B:1225-1487 lime

> color bynucleotide

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select /B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:1-155

1191 atoms, 1208 bonds, 155 residues, 1 model selected  

> color #1/B:261-261 lime

> color #1/B:556-556 magenta

> color #1/B:262-262 lime

> color #1/B:451-451 magenta

> select
> /B:281-286,313-315,319-322,330-334,345-349,355-360,363-368,377-382,391-394,407-413,418-423,437-447,450-455,460-462,526-528,532-537,563-571,579-584,601-605,610-614,618-623,1065-1068,1078-1084,1090-1095,1107-1112,1119-1125,1146-1149,1152-1158,1176-1180

1344 atoms, 1356 bonds, 164 residues, 1 model selected  

> select /B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:1-505

3853 atoms, 3927 bonds, 505 residues, 1 model selected  

> select /B:1071-1072

17 atoms, 18 bonds, 2 residues, 1 model selected  

> select /B:816-1072

1993 atoms, 2022 bonds, 257 residues, 1 model selected  

> select /B:1289-1290

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select /B:914-1290

2927 atoms, 2987 bonds, 377 residues, 1 model selected  

> select /B:1291-1292

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select /B:1286-1292

60 atoms, 61 bonds, 7 residues, 1 model selected  

> select /B:1281-1282

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select /B:1266-1282

134 atoms, 138 bonds, 17 residues, 1 model selected  

> select /B:1260

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:1238-1260

167 atoms, 173 bonds, 23 residues, 1 model selected  

> select /B:1236

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B:1216-1236

167 atoms, 167 bonds, 21 residues, 1 model selected  

> select /B:1187-1188

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B:1178-1188

84 atoms, 83 bonds, 11 residues, 1 model selected  

> select /B:1232

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /B:1218-1232

122 atoms, 121 bonds, 15 residues, 1 model selected  

> select /B:1239

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B:1235-1239

43 atoms, 42 bonds, 5 residues, 1 model selected  

> select /B:1227-1228

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /B:811-1228

3249 atoms, 3304 bonds, 418 residues, 1 model selected  

> select /B:1228

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B:1222-1228

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select /B:1228

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B:812-1228

3241 atoms, 3296 bonds, 417 residues, 1 model selected  

> select /B:766-812

360 atoms, 361 bonds, 47 residues, 1 model selected  

> select /B:406-812

3125 atoms, 3185 bonds, 407 residues, 1 model selected  

> select /B:1319

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B:1263-1319

469 atoms, 481 bonds, 57 residues, 1 model selected  

> select /B:1228

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B:1171-1228

434 atoms, 440 bonds, 58 residues, 1 model selected  

> select /B:1228-1229

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B:901-1229

2534 atoms, 2579 bonds, 329 residues, 1 model selected  

> select /B:900

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B:497-900

3114 atoms, 3167 bonds, 404 residues, 1 model selected  

> select /B:1228

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B:1-1228

9430 atoms, 9604 bonds, 1228 residues, 1 model selected  

> select /B:1417-1418

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B:1417-1422

51 atoms, 50 bonds, 6 residues, 1 model selected  

> select /B:1417

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:1417-1499

640 atoms, 646 bonds, 83 residues, 1 model selected  

> close session


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

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 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
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 7429.81.3
      OS Loader Version: 7429.81.3

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 10 days 19:25

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → UI
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: accepted → closed

Again, 'close' with a big structure. Okay, I am definitely changing the _cleanup() thing.

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