Opened 3 years ago

Closed 3 years ago

#7895 closed defect (nonchimerax)

Graphics crash, macOS 12.6, Intel Iris Plus Graphics 645

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data 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: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x0000000117bc8600 (most recent call first):
  File "/private/var/folders/4g/y2vpxwb56nb5dtyj0hs7b3tc0000gn/T/AppTranslocation/FF15D200-5F7E-4F22-AB73-D7F9537CE086/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/private/var/folders/4g/y2vpxwb56nb5dtyj0hs7b3tc0000gn/T/AppTranslocation/FF15D200-5F7E-4F22-AB73-D7F9537CE086/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/private/var/folders/4g/y2vpxwb56nb5dtyj0hs7b3tc0000gn/T/AppTranslocation/FF15D200-5F7E-4F22-AB73-D7F9537CE086/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/private/var/folders/4g/y2vpxwb56nb5dtyj0hs7b3tc0000gn/T/AppTranslocation/FF15D200-5F7E-4F22-AB73-D7F9537CE086/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/4g/y2vpxwb56nb5dtyj0hs7b3tc0000gn/T/AppTranslocation/FF15D200-5F7E-4F22-AB73-D7F9537CE086/d/ChimeraX-1.4.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" : 180000,
  "procLaunch" : "2022-10-27 10:47:50.5919 -0500",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,3",
  "procStartAbsTime" : 179407350251238,
  "coalitionID" : 3570,
  "osVersion" : {
    "train" : "macOS 12.6",
    "build" : "21G115",
    "releaseType" : "User"
  },
  "captureTime" : "2022-10-27 13:21:40.9720 -0500",
  "incident" : "3C299ADE-9CC6-49A3-B3B8-D36E9DA4CBDD",
  "bug_type" : "309",
  "pid" : 65480,
  "procExitAbsTime" : 184020452474036,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"73CA2261-731A-5BB6-95C8-1E07225606B2","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "3B408650-39A0-D6B0-B040-112A95B136B2",
  "wakeTime" : 50,
  "bridgeVersion" : {"build":"19P6067","train":"6.6"},
  "sleepWakeUUID" : "F09D872A-B4F8-4AA0-9F25-C20F0EA1CE87",
  "sip" : "enabled",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "ktriageinfo" : "VM - Fault hit memory shortage\n",
  "asi" : {"libsystem_c.dylib":["abort() called"]},
  "asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
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  "faultingThread" : 0,
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1280K       10 \nActivity Tracing                   256K        1 \nCG backing stores                 3120K        8 \nCG image                           528K       39 \nColorSync                          236K       28 \nCoreAnimation                     1560K      112 \nCoreGraphics                        16K        3 \nCoreUI image data                 4044K       49 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             1.4G      769 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            256K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nObjC additional data                15K        1 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        104K       26 \nStack                            163.7M       27 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      264.4M      164 \nVM_ALLOCATE (reserved)            32.0M        1         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            44.8M      687 \n__DATA_CONST                      32.6M      347 \n__DATA_DIRTY                      1641K      214 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       678.1M      157 \n__TEXT                           814.6M      687 \n__UNICODE                          592K        1 \ndyld private memory               1280K        3 \nmapped file                      524.9M       88 \nshared memory                     3516K       31 \n===========                     =======  ======= \nTOTAL                              4.1G     3476 \nTOTAL, minus reserved VM space     3.9G     3476 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    },
    {
      "rolloutId" : "60da5e84ab0ca017dace9abf",
      "factorPackIds" : {

      },
      "deploymentId" : 240000008
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
warning | Custom presets folder 'ui tool show "Model Panel"' does not exist  
  

> set bgColor white

> ~display atoms

> display cart

UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/zhouling95/Downloads/cryosparc_P439_J61_003_volume_map.mrc

Opened cryosparc_P439_J61_003_volume_map.mrc as #1, grid size 240,240,240,
pixel 0.94, shown at level 0.0843, step 1, values float32  

> ui tool show "Segment Map"

Segmenting cryosparc_P439_J61_003_volume_map.mrc, density threshold 0.084265  
Only showing 60 of 65 regions.  
Showing 60 of 65 region surfaces  
729 watershed regions, grouped to 65 regions  
Showing cryosparc_P439_J61_003_volume_map.seg - 65 regions, 60 surfaces  
Smoothing and grouping, standard deviation 5 voxels  
Showing 29 region surfaces  
Got 29 regions after smoothing 5 voxels.  
Smoothing and grouping, standard deviation 6 voxels  
Showing 16 region surfaces  
Got 16 regions after smoothing 6 voxels.  

> ui tool show "Model Panel"

> close #2

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> volume #1 level 0.05

> volume #1 level 0.08

Segmenting cryosparc_P439_J61_003_volume_map.mrc, density threshold 0.080000  
Only showing 60 of 65 regions.  
Showing 60 of 65 region surfaces  
729 watershed regions, grouped to 65 regions  
Showing cryosparc_P439_J61_003_volume_map.seg - 65 regions, 60 surfaces  
Smoothing and grouping, standard deviation 5 voxels  
Showing 29 region surfaces  
Got 29 regions after smoothing 5 voxels.  
Smoothing and grouping, standard deviation 6 voxels  
Showing 16 region surfaces  
Got 16 regions after smoothing 6 voxels.  
Grouped 15 regions  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

Opened cryosparc_P439_J61_003_volume_map_imasked as #3, grid size 240,240,240,
pixel 0.94, shown at step 1, values float32  

> hide #!2 models

> show #!2 models

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> vop threshold #3 minimum 0.081 set 0

Opened cryosparc_P439_J61_003_volume_map_imasked thresholded as #4, grid size
240,240,240, pixel 0.94, shown at step 1, values float32  

> vop threshold #4 maximum 0.081 set 1

Opened cryosparc_P439_J61_003_volume_map_imasked thresholded as #5, grid size
240,240,240, pixel 0.94, shown at step 1, values float32  

> hide #!2 models

> save "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/02 SARS-
> CoV-2-S2 Vaccine Design/amaro lab mutations/amaro_neg_mask_1.mrc" models #5

> show #!4 models

> show #!3 models

> close #3

> close #5

> close #4

> show #!2 models

Opened cryosparc_P439_J61_003_volume_map_imasked as #3, grid size 240,240,240,
pixel 0.94, shown at step 1, values float32  

> hide #!2 models

> vop threshold #3 minimum 0.081 set 0

Opened cryosparc_P439_J61_003_volume_map_imasked thresholded as #4, grid size
240,240,240, pixel 0.94, shown at step 1, values float32  

> vop threshold #4 maximum 0.081 set 1

Opened cryosparc_P439_J61_003_volume_map_imasked thresholded as #5, grid size
240,240,240, pixel 0.94, shown at step 1, values float32  

> save "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/02 SARS-
> CoV-2-S2 Vaccine Design/amaro lab mutations/amaro_pos_mask_1.mrc" models #5

> volume #5 level 0.06608

> open /Users/zhouling95/Downloads/cryosparc_P439_J67_000_volume_map_sharp.mrc

Opened cryosparc_P439_J67_000_volume_map_sharp.mrc as #6, grid size
240,240,240, pixel 0.94, shown at level 0.0709, step 1, values float32  

> surface dust #6 size 9.4

> volume #6 level 0.06329

> open /Users/zhouling95/Downloads/cryosparc_P439_J67_001_volume_map_sharp.mrc

Opened cryosparc_P439_J67_001_volume_map_sharp.mrc as #7, grid size
240,240,240, pixel 0.94, shown at level 0.112, step 1, values float32  

> surface dust #6 size 9.4

> surface dust #7 size 9.4

> open /Users/zhouling95/Downloads/cryosparc_P439_J61_002_volume_map_sharp.mrc

Opened cryosparc_P439_J61_002_volume_map_sharp.mrc as #8, grid size
240,240,240, pixel 0.94, shown at level 0.165, step 1, values float32  

> surface dust #8 size 9.4

> open
> /Users/zhouling95/Downloads/221026_S2_trimer_amaro_isolde_4_real_space_refined_058.pdb

Chain information for
221026_S2_trimer_amaro_isolde_4_real_space_refined_058.pdb #9  
---  
Chain | Description  
A B C | No description available  
  

> color #8 #d5d1d5 models transparency 0

> color #8 #d5d1d576 models

> graphics silhouettes true

> select #9/A:991

24 atoms, 25 bonds, 1 residue, 1 model selected  

> color sel red

> select #9/B:991

24 atoms, 25 bonds, 1 residue, 1 model selected  

> color sel red

> show sel atoms

> select #9/A:991

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #9/C:991

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel red

> select add #9

20409 atoms, 20637 bonds, 1323 residues, 1 model selected  

> select subtract #9

Nothing selected  

> volume #8 level 0.186

> open /Users/zhouling95/Downloads/cryosparc_P439_J68_003_volume_map_sharp.mrc

Opened cryosparc_P439_J68_003_volume_map_sharp.mrc as #10, grid size
240,240,240, pixel 0.94, shown at level 0.186, step 1, values float32  


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

Log:
Startup Messages  
---  
warning | Custom presets folder 'ui tool show "Model Panel"' does not exist  
  

> set bgColor white

> ~display atoms

> display cart

UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-18.8.5
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 1.7 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: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0)
      OS Loader Version: 540.120.3~22

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 9 days 22:02

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG ULTRAGEAR:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 202NTCZHP955
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.59


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash after opening MRC file

comment:2 by Tom Goddard, 3 years ago

Resolution: → nonchimerax
Status: assigned → closed
Summary: Crash after opening MRC file → Graphics crash, macOS 12.6, Intel Iris Plus Graphics 645

Apple Intel graphics driver crash.

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