Opened 3 years ago

Closed 3 years ago

#8914 closed defect (duplicate)

Crash in garbage collection

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core 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: 1.5 (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 0x00007ff85c96d680 (most recent call first):
  File "/Applications/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 "/Applications/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 "/Applications/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 "/Applications/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 "/Applications/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 "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/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" : 57000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,2",
  "coalitionID" : 2992,
  "osVersion" : {
    "train" : "macOS 13.2.1",
    "build" : "22D68",
    "releaseType" : "User"
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  "captureTime" : "2023-04-28 11:50:23.3214 +0200",
  "incident" : "F62B752F-E13D-4828-B0D1-DC8E767418C6",
  "pid" : 16255,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-04-28 11:00:43.9137 +0200",
  "procStartAbsTime" : 54641992286227,
  "procExitAbsTime" : 57621422916501,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"2686B579-F2BA-5CA2-BC16-7AD7FDA31E15","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "C0625BE1-D95D-72E9-69AB-D568A05B8865",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 3038,
  "bridgeVersion" : {"build":"20P3045","train":"7.2"},
  "sleepWakeUUID" : "347C9F50-598E-4AE0-9161-96704B746CF2",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140737486794583\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      shared memory            7fffffe83000-7fffffe84000 [    4K] r-x\/r-x SM=SHM  ",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140737486794583\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      shared memory            7fffffe83000-7fffffe84000 [    4K] r-x\/r-x SM=SHM  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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    "source" : "P",
    "arch" : "x86_64",
    "base" : 4311183360,
    "CFBundleShortVersionString" : "1.5.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 4096,
    "uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
    "path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.5.0.0"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703544864768,
    "size" : 609456,
    "uuid" : "bba77709-6cad-3592-ab03-09d0f7b8610e",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4397830144,
    "size" : 64028672,
    "uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
    "path" : "\/Applications\/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" : "x86_64",
    "base" : 4785373184,
    "size" : 165052416,
    "uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
    "path" : "\/Applications\/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"
  }
],
  "sharedCache" : {
  "base" : 140703544258560,
  "size" : 21474836480,
  "uuid" : "57815a20-af2c-3b56-9006-23abde7962b0"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                  960K        4 \nCG image                           424K       30 \nColorSync                          252K       29 \nCoreAnimation                      644K       19 \nCoreGraphics                        12K        2 \nCoreUI image data                 1740K       26 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                           649.0M      738 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                         92K       23 \nStack                            147.2M       24 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      167.8M      222 \nVM_ALLOCATE (reserved)            32.0M        1         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            46.3M      724 \n__DATA_CONST                      40.7M      378 \n__DATA_DIRTY                      1817K      223 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       211.2M      133 \n__OBJC_RO                         65.5M        1 \n__OBJC_RW                         1989K        2 \n__TEXT                           893.8M      731 \ndyld private memory                416K        3 \nmapped file                      526.6M       78 \nshared memory                     3008K       30 \n===========                     =======  ======= \nTOTAL                              3.0G     3446 \nTOTAL, minus reserved VM space     2.8G     3446 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "6297d96be2c9387df974efa4",
      "factorPackIds" : {

      },
      "deploymentId" : 240000008
    },
    {
      "rolloutId" : "6112e3d2fc54bc3389840661",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "64388cbd097a592d5667bdaf"
      },
      "deploymentId" : 240000402
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
      "experimentId" : "6317d2003d24842ff850182a",
      "deploymentId" : 400000013
    }
  ]
}
}
===== 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/emil/Downloads/J305_005_volume_map_half_A_deepEMhancer-
> sharpened_zflip.mrc

Opened J305_005_volume_map_half_A_deepEMhancer-sharpened_zflip.mrc as #1, grid
size 210,210,210, pixel 1.41, shown at level 0.000114, step 1, values float32  

> open /Users/emil/Downloads/AF-P20851-F1-model_v4_1-2.pdb

AF-P20851-F1-model_v4_1-2.pdb title:  
Alphafold monomer V2.0 prediction for C4B-binding protein β chain (P20851)
[more info...]  
  
Chain information for AF-P20851-F1-model_v4_1-2.pdb #2  
---  
Chain | Description | UniProt  
A | C4B-binding protein β chain | C4BPB_HUMAN  
  

> open /Users/emil/Library/CloudStorage/OneDrive-
> LundUniversity/Postdoc/Dahlbäck/Phenix/DockPredictedModel_56/AF-P07225-F1-model_v4_docked.pdb

Summary of feedback from opening /Users/emil/Library/CloudStorage/OneDrive-
LundUniversity/Postdoc/Dahlbäck/Phenix/DockPredictedModel_56/AF-P07225-F1-model_v4_docked.pdb  
---  
warning | Ignored bad PDB record found on line 460  
BREAK  
  
Chain information for AF-P07225-F1-model_v4_docked.pdb #3  
---  
Chain | Description  
A | No description available  
  

> volume #1 level 0.01236

> select add #2

882 atoms, 906 bonds, 114 residues, 1 model selected  

> select add #3

4046 atoms, 4128 bonds, 4 pseudobonds, 518 residues, 3 models selected  

> select subtract #2

3164 atoms, 3222 bonds, 4 pseudobonds, 404 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select add #2

882 atoms, 906 bonds, 114 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,168.1,0,1,0,170.13,0,0,1,204.08

> view matrix models #2,1,0,0,203.23,0,1,0,163.07,0,0,1,145.98

> hide #2 models

> hide #!3 models

> view #3 clip false

> volume #1 level 0.1073

> volume #1 level 0.05829

> volume #1 style mesh

> show #!3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:451

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:451-474

187 atoms, 188 bonds, 1 pseudobond, 22 residues, 2 models selected  

> select clear

> select
> #3/A:255-259,262-266,273-275,282-284,312-318,324-331,336-343,349-355,358-364,369-374,384-390,394-399,402-408,420-427,448-451,479-481,484-486,491-493,507-516,521-528,535-541,548-554,557-562,573-580,584-587,615-619,637-644,665-667

1330 atoms, 1328 bonds, 166 residues, 1 model selected  

> select #3/A:451-474

187 atoms, 188 bonds, 1 pseudobond, 22 residues, 2 models selected  

> select #3/A:460

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/A:460-468

56 atoms, 54 bonds, 1 pseudobond, 7 residues, 2 models selected  

> select #3/A:469

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

> select #3/A:469-471

27 atoms, 26 bonds, 3 residues, 1 model selected  

> select #3/A:460

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/A:460-478

138 atoms, 137 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select #3/A:414-415

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A:414-458

370 atoms, 379 bonds, 45 residues, 1 model selected  

> select #3/A:319

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

> select #3/A:319-340

187 atoms, 191 bonds, 22 residues, 1 model selected  

> select #3/A:342

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

> select #3/A:342-354

103 atoms, 105 bonds, 13 residues, 1 model selected  

> select #3/A:313

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

> select #3/A:313-320

71 atoms, 72 bonds, 8 residues, 1 model selected  

> select
> #3/A:255-259,262-266,273-275,282-284,312-318,324-331,336-343,349-355,358-364,369-374,384-390,394-399,402-408,420-427,448-451,479-481,484-486,491-493,507-516,521-528,535-541,548-554,557-562,573-580,584-587,615-619,637-644,665-667

1330 atoms, 1328 bonds, 166 residues, 1 model selected  

> select clear

> select #3/A:313

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

> select #3/A:313-318

54 atoms, 55 bonds, 6 residues, 1 model selected  

> volume #1 level 0.02155

> select #3/A:296

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

> select #3/A:296

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

> select #3/A:298

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

> select #3/A:298

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

> select #3/A:296,298

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

> select #3/A:296,298,335

27 atoms, 24 bonds, 3 residues, 1 model selected  

> select #3/A:296,298,335

27 atoms, 24 bonds, 3 residues, 1 model selected  

> select #3/A:296,298,335

27 atoms, 24 bonds, 3 residues, 1 model selected  

> select #3/A:296,298,333,335

35 atoms, 31 bonds, 4 residues, 1 model selected  

> select #3/A:296,298,333,335,451

46 atoms, 41 bonds, 5 residues, 1 model selected  

> select #3/A:296,298,333,335,451,464

55 atoms, 49 bonds, 6 residues, 1 model selected  

> select #3/A:296,298,333,335,451,464-465

64 atoms, 58 bonds, 7 residues, 1 model selected  

> hide #!1 models

> show #!1 models

> open /Users/emil/Downloads/unrelaxed_model_5.pdb

Chain information for unrelaxed_model_5.pdb #4  
---  
Chain | Description  
A | No description available  
  

> view #4 clip false

> view #1 clip false

> hide #!1 models

> hide #!3 models

> hide #!4 models

> select add #3

3164 atoms, 3222 bonds, 4 pseudobonds, 404 residues, 2 models selected  

> select subtract #3

Nothing selected  

> show #2 models

> view #1 clip false

No displayed objects specified.  

> select add #2

882 atoms, 906 bonds, 114 residues, 1 model selected  

> view #1 clip false

No displayed objects specified.  

> select clear

> show #!1 models

> hide #!1 models

> show #!3 models

> show #!1 models

> hide #2 models

> view #3 clip false

> hide #!3 models

> show #2 models

> hide #!1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:23

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

> select #2/A:23-26

30 atoms, 30 bonds, 4 residues, 1 model selected  

> select clear

> select #2/A:80

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:80-136

441 atoms, 455 bonds, 57 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #2

441 atoms, 450 bonds, 57 residues, 1 model selected  

> show #!1 models

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.98625,0.084404,0.14211,204.1,0.10572,-0.98304,-0.14985,189.6,0.12705,0.16281,-0.97844,114.43

> volume #1 style surface

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.98625,0.084404,0.14211,154.6,0.10572,-0.98304,-0.14985,179.2,0.12705,0.16281,-0.97844,117.95

> view matrix models
> #2,0.98625,0.084404,0.14211,149.66,0.10572,-0.98304,-0.14985,166,0.12705,0.16281,-0.97844,107.24

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.9045,-0.13279,0.40529,157.58,-0.22996,-0.95216,0.20125,174.44,0.35918,-0.27523,-0.89176,112.27

> ui tool show "Fit in Map"

Opened AF-P20851-F1-model_v4_1-2.pdb map 5 as #5, grid size 35,42,37, pixel
1.67, shown at level 0.0742, step 1, values float32  

> fitmap #2 inMap #1 resolution 5

Fit map AF-P20851-F1-model_v4_1-2.pdb map 5 in map
J305_005_volume_map_half_A_deepEMhancer-sharpened_zflip.mrc using 1841 points  
correlation = 0.5553, correlation about mean = 0.143, overlap = 70.84  
steps = 168, shift = 6.2, angle = 36.4 degrees  
  
Position of AF-P20851-F1-model_v4_1-2.pdb map 5 (#5) relative to
J305_005_volume_map_half_A_deepEMhancer-sharpened_zflip.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98809918 -0.11371702 -0.10357822 142.85552251  
-0.03728139 -0.83035603 0.55598467 173.79678662  
-0.14923172 -0.54550646 -0.82471365 121.02467929  
Axis -0.99674931 0.04131226 0.06916729  
Axis point 0.00000000 109.48067971 38.40353747  
Rotation angle (degrees) 146.45844004  
Shift along axis -126.84025462  
  
Average map value = 0.1286 for 441 atoms, 159 outside contour  

> volume #1 style mesh

> view

> view matrix models
> #2,0.5372,0.59259,0.60021,147.42,-0.43903,0.80406,-0.40091,140.64,-0.72019,-0.048141,0.69211,141.5

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.5372,0.59259,0.60021,149.55,-0.43903,0.80406,-0.40091,141.89,-0.72019,-0.048141,0.69211,143.15

> view matrix models
> #2,0.5372,0.59259,0.60021,152.65,-0.43903,0.80406,-0.40091,140.08,-0.72019,-0.048141,0.69211,143.23

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.61799,0.77851,0.10958,142.05,-0.71357,0.61394,-0.33747,147.12,-0.33,0.13036,0.93494,139.25

> fitmap #2 inMap #1 resolution 5

Fit map AF-P20851-F1-model_v4_1-2.pdb map 5 in map
J305_005_volume_map_half_A_deepEMhancer-sharpened_zflip.mrc using 1841 points  
correlation = 0.6123, correlation about mean = 0.2914, overlap = 71.07  
steps = 168, shift = 4.83, angle = 30.5 degrees  
  
Position of AF-P20851-F1-model_v4_1-2.pdb map 5 (#5) relative to
J305_005_volume_map_half_A_deepEMhancer-sharpened_zflip.mrc (#1) coordinates:  
Matrix rotation and translation  
0.65749808 0.68154678 0.32123239 144.13222803  
-0.33923215 0.64846361 -0.68148110 134.16274531  
-0.67276877 0.33910016 0.65756616 139.14639038  
Axis 0.58232344 0.56715736 -0.58243622  
Axis point 271.35425799 -7.63192591 -0.00000000  
Rotation angle (degrees) 61.19932943  
Shift along axis 78.97906442  
  
Average map value = 0.149 for 441 atoms, 139 outside contour  

> select clear

> select #2/A:33

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

> select #2/A:33

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

> select #2/A:35

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

> select #2/A:35

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

> select #2/A:33,35

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select #2/A:33,35,48

22 atoms, 19 bonds, 3 residues, 1 model selected  

> select #2/A:33,35,48,50

30 atoms, 26 bonds, 4 residues, 1 model selected  

> show #!3 models

> select add #2

441 atoms, 450 bonds, 57 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.6575,0.68155,0.32123,146.15,-0.33923,0.64846,-0.68148,133.87,-0.67277,0.3391,0.65757,138.67

> select clear

> select #2/A:33,35,48,50

30 atoms, 26 bonds, 4 residues, 1 model selected  

> show sel target ab

> hide #!1 models

> hide #2 models

> hide #!3 models

> show #!4 models

> select add #2

441 atoms, 450 bonds, 57 residues, 1 model selected  

> select add #4

6301 atoms, 6431 bonds, 1 pseudobond, 811 residues, 3 models selected  

> view matrix models
> #2,0.6575,0.68155,0.32123,273.06,-0.33923,0.64846,-0.68148,329.8,-0.67277,0.3391,0.65757,160.4,#4,1,0,0,126.9,0,1,0,195.93,0,0,1,21.73

> ui tool show "Show Sequence Viewer"

> sequence chain #4/A

Alignment identifier is 4/A  

> select #4/A:1-2

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

> select #4/A:1-103

812 atoms, 827 bonds, 103 residues, 1 model selected  

> select #4/A:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #4/A:1-152

1180 atoms, 1204 bonds, 152 residues, 1 model selected  

> select #4/A:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #4/A:1-204

1577 atoms, 1607 bonds, 204 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show #!1 models

> show #2 models

> show #!3 models

> hide #!1 models

> hide #!3 models

> hide #!4 models

> close #2


===== 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 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

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: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2,7 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
      OS Loader Version: 564.40.4~66

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 6 days, 2 hours, 43 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        HP E24q G4:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: CNK15108PQ  
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


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

Component: Unassigned → Core
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

The delayed call of _cleanup has been eliminated for just this reason.

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