Graphics crash, macOS 12.2.1, Intel Iris Plus Graphics

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x0000000116924600 (most recent call first):
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.3.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" : 100000,
  "procLaunch" : "2022-05-27 21:31:41.4884 -0700",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 974925406,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,2",
  "procStartAbsTime" : 81571600881534,
  "coalitionID" : 8324,
  "osVersion" : {
    "train" : "macOS 12.2.1",
    "build" : "21D62",
    "releaseType" : "User"
  },
  "captureTime" : "2022-05-28 03:29:18.1560 -0700",
  "incident" : "871B7822-74EF-4640-BF28-95559B90414F",
  "bug_type" : "309",
  "pid" : 38079,
  "procExitAbsTime" : 103028561528852,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"E5C324D9-64F9-5D64-BF03-E50A2944A6D5","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "AF0910C3-1DE1-80F6-8480-3B6BA4A01CC0",
  "wakeTime" : 39424,
  "bridgeVersion" : {"build":"19P744","train":"6.2"},
  "sleepWakeUUID" : "4E60448F-FF12-4D18-AB2D-AF928B1E6B0E",
  "sip" : "enabled",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "asi" : {"libsystem_c.dylib":["abort() called"]},
  "asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
  "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" : 34,
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(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               768K        6 \nActivity Tracing                   256K        1 \nCG backing stores                 2880K        8 \nCG image                           348K       52 \nColorSync                          244K       28 \nCoreAnimation                     1184K       70 \nCoreGraphics                        16K        3 \nCoreUI image data                 5168K       52 \nFoundation                          36K        2 \nKernel Alloc Once                   12K        2 \nMALLOC                           962.7M     1123 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            640K        2         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        40K        5 \nOpenCL                           235.5M       85 \nOpenCL (reserved)                   52K        6         reserved VM address space (unallocated)\nOpenGL GLSL                        384K        4 \nSTACK GUARD                       56.1M       36 \nStack                            145.8M       36 \nVM_ALLOCATE                      189.9M      201 \nVM_ALLOCATE (reserved)           128.0M        3         reserved VM address space (unallocated)\n__DATA                            44.3M      762 \n__DATA_CONST                      31.7M      343 \n__DATA_DIRTY                      1639K      218 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       749.2M      219 \n__OBJC_RO                         81.8M        1 \n__OBJC_RW                         3136K        2 \n__TEXT                           870.0M      744 \n__UNICODE                          588K        1 \ndyld private memory               1056K        3 \nmapped file                      546.1M       71 \nshared memory                     3656K       33 \n===========                     =======  ======= \nTOTAL                              4.2G     4133 \nTOTAL, minus reserved VM space     3.8G     4133 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "queue" : "opencl_runtime"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "602ad4dac86151000cf27e46",
      "factorPackIds" : {
        "SIRI_DICTATION_ASSETS" : "6193d03f2171a2330e561dfc"
      },
      "deploymentId" : 240000305
    },
    {
      "rolloutId" : "60da5e84ab0ca017dace9abf",
      "factorPackIds" : {

      },
      "deploymentId" : 240000008
    },
    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
      },
      "deploymentId" : 240000066
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    {
      "rolloutId" : "601d9415f79519000ccd4b69",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
      },
      "deploymentId" : 240000414
    },
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000015
    },
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000370
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000149
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/fli05/Documents/Phenix/CB1_Fab52515/RealSpaceRefine_11/J883_real_space_refined_011-coot-0.pdb
> format pdb

Chain information for J883_real_space_refined_011-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
H | No description available  
L | No description available  
  

> open /Users/fli05/Library/CloudStorage/OneDrive-
> Amgen/CB1/EM/CB1_Fab52515/FinalMap/cryosparc_P11_J883_010_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.813, shown at level 0.0332, step 2, values float32  

> ui tool show ISOLDE

> set selectionWidth 4

Removed all altlocs in #1 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 35 residues in model #1 to IUPAC-IUB
standards.  
Chain information for J883_real_space_refined_011-coot-0.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/H | No description available  
1.2/L | No description available  
  
Done loading forcefield  

> clipper associate #2 toModel #1

Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #1.1.1.1, grid size
400,400,400, pixel 0.813, shown at step 1, values float32  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to
J883_real_space_refined_011-coot-0.pdb #1.2  
---  
warnings | Not adding hydrogens to /A GLU 100 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLN 115 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LEU 117 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 145 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 183 CB because it is missing heavy-atom bond
partners  
4 messages similar to the above omitted  
notes | No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb
(#1.2) chain A; guessing termini instead  
No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb (#1.2)
chain H; guessing termini instead  
No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb (#1.2)
chain L; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 100, /H GLN 1, /L ASP
128  
Chain-initial residues that are not actual N termini: /A ASN 112, /A ALA 335  
Chain-final residues that are actual C termini: /H SER 127, /L ARG 235  
Chain-final residues that are not actual C termini: /A PHE 412, /A MET 103, /A
SER 303  
404 hydrogen bonds  
Adding 'H' to /A ASN 112  
Adding 'H' to /A ALA 335  
/A PHE 412 is not terminus, removing H atom from 'C'  
4026 hydrogens added  
  

> hide HC

> select up

453 atoms, 454 bonds, 30 residues, 1 model selected  

> select up

4465 atoms, 4524 bonds, 275 residues, 1 model selected  
Loading residue template for ZDG from internal database  
ISOLDE: stopped sim  

> select clear

> select up

61 atoms, 64 bonds, 1 residue, 1 model selected  

> isolde parameterise sel

Residue name ZDG already corresponds to template MC_ZDG in the amber14
forcefield. If you wish to replace that template, re-run this command with
override=True  

> select up

61 atoms, 64 bonds, 1 residue, 1 model selected  

> select up

4465 atoms, 4524 bonds, 275 residues, 1 model selected  

> select down

61 atoms, 64 bonds, 1 residue, 1 model selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> select up

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select up

534 atoms, 544 bonds, 30 residues, 1 model selected  

> select up

4404 atoms, 4458 bonds, 274 residues, 1 model selected  
ISOLDE: stopped sim  

> save /Users/fli05/Desktop/CB1.pdb

> close session

Fetching CCD LEU_LL from http://ligand-
expo.rcsb.org/reports/L/LEU_LL/LEU_LL.cif  
Fetching CCD LEU_LEO2 from http://ligand-
expo.rcsb.org/reports/L/LEU_LEO2/LEU_LEO2.cif  
Fetching CCD LEU_LFZW from http://ligand-
expo.rcsb.org/reports/L/LEU_LFZW/LEU_LFZW.cif  
Fetching CCD LAY from http://ligand-expo.rcsb.org/reports/L/LAY/LAY.cif  
Traceback (most recent call last):  
File "/Users/fli05/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 180, in
_show_selected_unparameterised_residue  
residue.atoms.displays = True  
File "atomic_cpp/cymol.pyx", line 994, in
chimerax.atomic.cymol.CyResidue.atoms.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "atomic_cpp/cymol.pyx", line 994, in
chimerax.atomic.cymol.CyResidue.atoms.__get__  
  
See log for complete Python traceback.  
  

> open
> /Users/fli05/Documents/Phenix/CB1_Fab52515/RealSpaceRefine_11/J883_real_space_refined_011-coot-0.pdb
> format pdb

Chain information for J883_real_space_refined_011-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
H | No description available  
L | No description available  
  
Removed all altlocs in #1 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 35 residues in model #1 to IUPAC-IUB
standards.  
Chain information for J883_real_space_refined_011-coot-0.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/H | No description available  
1.2/L | No description available  
  

> open /Users/fli05/Library/CloudStorage/OneDrive-
> Amgen/CB1/EM/CB1_Fab52515/FinalMap/cryosparc_P11_J883_010_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.813, shown at level 0.0332, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.2481

Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #1.1.1.1, grid size
400,400,400, pixel 0.813, shown at step 1, values float32  

> addh

Summary of feedback from adding hydrogens to
J883_real_space_refined_011-coot-0.pdb #1.2  
---  
warnings | Not adding hydrogens to /A GLU 100 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLN 115 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LEU 117 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 145 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 183 CB because it is missing heavy-atom bond
partners  
4 messages similar to the above omitted  
notes | No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb
(#1.2) chain A; guessing termini instead  
No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb (#1.2)
chain H; guessing termini instead  
No usable SEQRES records for J883_real_space_refined_011-coot-0.pdb (#1.2)
chain L; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 100, /H GLN 1, /L ASP
128  
Chain-initial residues that are not actual N termini: /A ASN 112, /A ALA 335  
Chain-final residues that are actual C termini: /H SER 127, /L ARG 235  
Chain-final residues that are not actual C termini: /A PHE 412, /A MET 103, /A
SER 303  
404 hydrogen bonds  
Adding 'H' to /A ASN 112  
Adding 'H' to /A ALA 335  
/A PHE 412 is not terminus, removing H atom from 'C'  
4026 hydrogens added  
  

> hide HC

> select #1

8050 atoms, 8158 bonds, 2 pseudobonds, 510 residues, 13 models selected  
ISOLDE: stopped sim  
Fetching CCD ZDG from http://ligand-expo.rcsb.org/reports/Z/ZDG/ZDG.cif  

> select up

453 atoms, 454 bonds, 30 residues, 1 model selected  

> select up

4465 atoms, 4524 bonds, 275 residues, 1 model selected  
ISOLDE: stopped sim  
Deleted the following atoms from residue ZDG A2110: HBB1, HAU, HBG2, HAV, HBD,
HBI1, HBK1, HAD1, HBI2, HBB3, HAD2, HAK, HAJ, HBJ1, HAM, HBB2, HBK2, HAX, HAE,
HAN, HBH1, HBJ2, HBH2, HBG1  

> close session

> open /Users/fli05/Desktop/CB1.pdb format pdb

Chain information for CB1.pdb #1  
---  
Chain | Description  
A | No description available  
H | No description available  
L | No description available  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for CB1.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/H | No description available  
1.2/L | No description available  
  

> open /Users/fli05/Library/CloudStorage/OneDrive-
> Amgen/CB1/EM/CB1_Fab52515/FinalMap/cryosparc_P11_J883_010_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.813, shown at level 0.0332, step 2, values float32  
Opened cryosparc_P11_J883_010_volume_map_sharp.mrc as #1.1.1.1, grid size
400,400,400, pixel 0.813, shown at step 1, values float32  

> addh

Summary of feedback from adding hydrogens to CB1.pdb #1.2  
---  
warnings | Not adding hydrogens to /A GLU 100 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLN 115 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LEU 117 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 145 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 183 CB because it is missing heavy-atom bond
partners  
4 messages similar to the above omitted  
notes | No usable SEQRES records for CB1.pdb (#1.2) chain A; guessing termini
instead  
No usable SEQRES records for CB1.pdb (#1.2) chain H; guessing termini instead  
No usable SEQRES records for CB1.pdb (#1.2) chain L; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 100, /H GLN 1, /L ASP
128  
Chain-initial residues that are not actual N termini: /A ASN 112, /A ALA 335  
Chain-final residues that are actual C termini: /H SER 127, /L ARG 235  
Chain-final residues that are not actual C termini: /A PHE 412, /A MET 103, /A
SER 303  
386 hydrogen bonds  
/A PHE 412 is not terminus, removing H atom from 'C'  
2 hydrogens added  
  

> hide HC

> select up

453 atoms, 454 bonds, 30 residues, 1 model selected  

> select up

4406 atoms, 4460 bonds, 274 residues, 1 model selected  

Populating font family aliases took 386 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: started sim  


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)
      OS Loader Version: 540.80.2~11

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 2 days 29 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      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

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    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: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Tom Goddard]

Apple graphics driver crash. Running ISOLDE simulation.