Opened 2 years ago

Closed 2 years ago

#9442 closed defect (can't reproduce)

Crash deleting tool

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

Description 

The following bug report has been submitted:
Platform:        macOS-13.0-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: Bus error

Current thread 0x00000001e3066500 (most recent call first):
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2301 in destroy
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2165 in _destroy
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 772 in remove_tool
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 335 in remove_tool
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 292 in reset_state
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 541 in reset
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 700 in restore
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 1004 in open
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 26 in open
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 428 in remember_data_format
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 458 in collated_open
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 193 in provider_open
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 162 in _qt_safe
  File "/Volumes/ChimeraXInstaller/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 "/Volumes/ChimeraXInstaller/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 "/Volumes/ChimeraXInstaller/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 "/Volumes/ChimeraXInstaller/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Volumes/ChimeraXInstaller/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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  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4373135360,
    "CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 2555904,
    "uuid" : "5ee765c2-b52f-3980-9781-73db1abd2bde",
    "path" : "\/Volumes\/VOLUME\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.9.11"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4842356736,
    "size" : 1654784,
    "uuid" : "fc338cc4-c4ac-3763-85b1-52ada2adfe1a",
    "path" : "\/Volumes\/VOLUME\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtCore.abi3.so",
    "name" : "QtCore.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4474454016,
    "size" : 4587520,
    "uuid" : "7b11213a-bd62-384b-9835-2bf9bacff4a0",
    "path" : "\/Volumes\/VOLUME\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
    "name" : "QtCore"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5005721600,
    "size" : 622592,
    "uuid" : "a07d6b8c-b467-339b-8483-3ba6dc00495e",
    "path" : "\/Volumes\/VOLUME\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6569541632,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5079040,
    "uuid" : "da41d167-77ad-3bee-8a4c-ccc1399ee15e",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1953.1"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6727622656,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3358720,
    "uuid" : "8384f6fe-bb4d-3b01-b6b4-54011042b722",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6622621696,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15761408,
    "uuid" : "47f20729-e102-3a52-a31d-8be7277f85fb",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2299"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4364976128,
    "CFBundleShortVersionString" : "1.5.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
    "uuid" : "a5992708-d5b4-36ec-ac0a-e525f6105b56",
    "path" : "\/Volumes\/VOLUME\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.5.0.0"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6565814272,
    "size" : 566452,
    "uuid" : "b7142778-f6ba-31ca-820c-34b24d90f149",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5712642048,
    "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"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4484120576,
    "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"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  }
],
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=1.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.6G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               768K        6 \nActivity Tracing                   256K        1 \nCG backing stores                 1344K        4 \nCG image                           944K       45 \nColorSync                          640K       29 \nCoreAnimation                      800K       38 \nCoreGraphics                        48K        3 \nCoreServices                       432K        3 \nCoreUI image data                 4032K       37 \nDispatch continuations            96.0M        1 \nFoundation                         208K        3 \nKernel Alloc Once                   32K        1 \nMALLOC                           756.9M      402 \nMALLOC guard page                  192K       11 \nMALLOC_MEDIUM (reserved)         120.0M        1         reserved VM address space (unallocated)\nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        608K       38 \nStack                            162.9M       39 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      273.3M      369 \nVM_ALLOCATE (reserved)           256.0M        1         reserved VM address space (unallocated)\n__AUTH                            1903K      358 \n__AUTH_CONST                      24.6M      587 \n__CTF                               756        1 \n__DATA                            20.0M      719 \n__DATA_CONST                      37.1M      727 \n__DATA_DIRTY                      1983K      229 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       790.8M      140 \n__OBJC_CONST                      4707K      323 \n__OBJC_RO                         65.1M        1 \n__OBJC_RW                         1981K        1 \n__TEXT                           803.2M      749 \ndyld private memory                416K        3 \nmapped file                      226.7M       58 \nshared memory                     3248K       28 \n===========                     =======  ======= \nTOTAL                              3.6G     4965 \nTOTAL, minus reserved VM space     3.3G     4965 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "62b4513af75dc926494899c6",
      "factorPackIds" : {
        "COREOS_ICD" : "62fbe3cfa9a700130f60b3ea"
      },
      "deploymentId" : 240000019
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000298
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
      "experimentId" : "6317d2003d24842ff850182a",
      "deploymentId" : 400000013
    }
  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== 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/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__UBP41_HUMAN__998aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb"

Chain information for
MYB_HUMAN__UBP41_HUMAN__998aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "/Users/jrutter/Dropbox (MIT)/Ebert
> Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__UBP41_HUMAN__998aa_scores_rank_001_alphafold2_multimer_v3_model_3_seed_000
> 2.json"

> color #1/A:620-640 lime

> color #1/B:27-356 magenta

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__RN216_HUMAN__1506aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb"

Chain information for
MYB_HUMAN__RN216_HUMAN__1506aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #1 models

> color #2 bypolymer

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "/Users/jrutter/Dropbox (MIT)/Ebert
> Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__RN216_HUMAN__1506aa_scores_rank_001_alphafold2_multimer_v3_model_5_seed_000.json"

Number of residues in structure
"MYB_HUMAN__UBP41_HUMAN__998aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#1" is 998 which does not match PAE matrix size 1506.  
  
This can happen if chains were deleted from the AlphaFold model or if the PAE
data was applied to a structure that was not the one predicted by AlphaFold.
Use the full-length AlphaFold model to show predicted aligned error.  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #2 file "/Users/jrutter/Dropbox (MIT)/Ebert
> Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__RN216_HUMAN__1506aa_scores_rank_001_alphafold2_multimer_v3_model_5_seed_000.json"

> color #2/A:20-287 lime

> color #2/B:306-848 magenta

> alphafold pae #2 colorDomains true

> color bfactor #2 palette alphafold

12068 atoms, 1506 residues, atom bfactor range 13.1 to 97.1  

> color #2 bychain

> alphafold contacts #2/A toResidues #2/B

> color bfactor #2 palette alphafold

12068 atoms, 1506 residues, atom bfactor range 13.1 to 97.1  

> color #!2 bypolymer

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__FBX7_HUMAN__1162aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb"

Chain information for
MYB_HUMAN__FBX7_HUMAN__1162aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close #2

> color #3 bychain

> alphafold contacts #2/A toResidues #2/B

No residues specified for alphafold contacts  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #3 file "/Users/jrutter/Dropbox (MIT)/Ebert
> Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__FBX7_HUMAN__1162aa_scores_rank_001_alphafold2_multimer_v3_model_2_seed_000.json"

> alphafold contacts #2/A toResidues #2/B

No residues specified for alphafold contacts  

> alphafold contacts #2/A toResidues #2/B

No residues specified for alphafold contacts  

> color #3/A:159-159 lime

> color #3/A:325-325 magenta

> color #3/A:621-640/B:1-113 magenta

> alphafold pae #3 colorDomains true

> color bfactor #3 palette alphafold

9209 atoms, 1162 residues, atom bfactor range 12.5 to 97.9  

> alphafold contacts #2/A toResidues #2/B

No residues specified for alphafold contacts  

> color bfactor #3 palette alphafold

9209 atoms, 1162 residues, atom bfactor range 12.5 to 97.9  

> color #3/A:23-215 lime

> color #3/B:17-76 magenta

> alphafold contacts #2/A toResidues #2/B

No residues specified for alphafold contacts  

> alphafold contacts #2/A toResidues #2/B

No residues specified for alphafold contacts  

> contacts#2/A to #2/B

Unknown command: alphafold contacts#2/A to #2/B  

> alphafold contacts #2/A toResidues #2/B distance 4

No residues specified for alphafold contacts  

> select add #3

9209 atoms, 9443 bonds, 1162 residues, 1 model selected  

> alphafold contacts #2/A toResidues #2/B distance 4

No residues specified for alphafold contacts  

> color bfactor #3 palette alphafold

9209 atoms, 1162 residues, atom bfactor range 12.5 to 97.9  

> alphafold contacts #2/A toResidues #2/B distance 4

No residues specified for alphafold contacts  

> undo

Undo failed, probably because structures have been modified.  

> undo

Undo failed, probably because structures have been modified.  

> undo

Undo failed, probably because structures have been modified.  

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__NOSIP_HUMAN__941aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb"

Chain information for
MYB_HUMAN__NOSIP_HUMAN__941aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close #3

> color #2 bypolymer

> color #2 bychain

> ui tool show "AlphaFold Error Plot"

Must choose structure to associate with predicted aligned error  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #2 file "/Users/jrutter/Dropbox (MIT)/Ebert
> Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__NOSIP_HUMAN__941aa_scores_rank_001_alphafold2_multimer_v3_model_1_seed_000.json"

> color #2/A:192-192 lime

> color #2/A:65-65 magenta

> alphafold pae #2 colorDomains true

> color #2 bypolymer

> color #2 bychain

> color #2 bypolymer

> show #2 surfaces

> alphafold contacts #2/A toResidues #2/B distance 4

> select coil

10503 atoms, 10711 bonds, 4 pseudobonds, 1357 residues, 3 models selected  

> hide sel & #!2 surfaces

> select all

15398 atoms, 15761 bonds, 66 pseudobonds, 1939 residues, 3 models selected  

> transparency (#!2 & sel) 60

> hide #2.3 models

> ui windowfill toggle

> show sel & #!2 atoms

> mlp sel & #!2

Map values for surface
"MYB_HUMAN__NOSIP_HUMAN__941aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_A
SES surface": minimum -30.39, mean -5.152, maximum 25.31  
Map values for surface
"MYB_HUMAN__NOSIP_HUMAN__941aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B
SES surface": minimum -26.91, mean -4.538, maximum 22.45  
To also show corresponding color key, enter the above mlp command and add key
true  

> select coil

10503 atoms, 10711 bonds, 4 pseudobonds, 1357 residues, 3 models selected  

> hide sel & #!2 atoms

> hide sel & #!2 surfaces

> ui windowfill toggle

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__NUSAP_HUMAN__1081aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb"

Chain information for
MYB_HUMAN__NUSAP_HUMAN__1081aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select add #2

12789 atoms, 13059 bonds, 66 pseudobonds, 1630 residues, 5 models selected  

> hide #!2 models

> select subtract #2

5378 atoms, 5478 bonds, 689 residues, 3 models selected  

> hide #2.1 models

> hide #2.2 models

> color #3 bychain

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__KLH41_HUMAN__1246aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb"

Chain information for
MYB_HUMAN__KLH41_HUMAN__1246aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #3 models

> color #4 bychain

> color #4 bypolymer

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__FBXL8_HUMAN__1014aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb"

Chain information for
MYB_HUMAN__FBXL8_HUMAN__1014aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #4 models

> color #5 bypolymer

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__UBE3A_HUMAN__1515aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb"

Chain information for
MYB_HUMAN__UBE3A_HUMAN__1515aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #6 models

> show #6 models

> hide #5 models

> color #6 bypolymer

> color #6 bychain

> close #6

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__UBE3C_HUMAN__1723aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb"

Chain information for
MYB_HUMAN__UBE3C_HUMAN__1723aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color #6 bychain

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__RFPLB_HUMAN__903aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb"

Chain information for
MYB_HUMAN__RFPLB_HUMAN__903aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #6 models

> color #7 bypolymer

> color #7 bychain

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__KLH41_HUMAN__1246aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb"

Chain information for
MYB_HUMAN__KLH41_HUMAN__1246aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #7 models

> color #8 bypolymer

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__MEX3C_HUMAN__1299aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"

Chain information for
MYB_HUMAN__MEX3C_HUMAN__1299aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #8 models

> color #9 bychain

> color #9 bypolymer

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__EP300_HUMAN__3054aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb"

Chain information for
MYB_HUMAN__EP300_HUMAN__3054aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #9 models

> color #10 bypolymer

> color #10 bychain

> view sel

> hide #10 models

> open "/Users/jrutter/Dropbox (MIT)/MYB_KIFC1_cleanup.cxs"


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

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/jrutter/Dropbox (MIT)/MYB_KIFC1_cleanup.cxs"

Log from Sat Jul 22 22:07:52 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

Populating font family aliases took 137 ms. Replace uses of missing font
family "Lato" with one that exists to avoid this cost.  

> alphafold predict
> MEDEEGPEYGKPDFVLLDQVTMEDFMRNLQLRFEKGRIYTYIGEVLVSVNPYQELPLYGPEAIARYQGRELYERPPHLYAVANAAYKAMKHRSRDTCIVISGESGAGKTEASKHIMQYIAAVTNPSQRAEVERVKDVLLKSTCVLEAFGNARTNRNHNSSRFGKYMDINFDFKGDPIGGHIHSYLLEKSRVLKQHVGERNFHAFYQLLRGSEDKQLHELHLERNPAVYNFTHQGAGLNMTVHSALDSDEQSHQAVTEAMRVIGFSPEEVESVHRILAAILHLGNIEFVETEEGGLQKEGLAVAEEALVDHVAELTATPRDLVLRSLLARTVASGGRELIEKGHTAAEASYARDACAKAVYQRLFEWVVNRINSVMEPRGRDPRRDGKDTVIGVLDIYGFEVFPVNSFEQFCINYCNEKLQQLFIQLILKQEQEEYEREGITWQSVEYFNNATIVDLVERPHRGILAVLDEACSSAGTITDRIFLQTLDMHHRHHLHYTSRQLCPTDKTMEFGRDFRIKHYAGDVTYSVEGFIDKNRDFLFQDFKRLLYNSTDPTLRAMWPDGQQDITEVTKRPLTAGTLFKNSMVALVENLASKEPFYVRCIKPNEDKVAGKLDENHCRHQVAYLGLLENVRVRRAGFASRQPYSRFLLRYKMTCEYTWPNHLLGSDKAAVSALLEQHGLQGDVAFGHSKLFIRSPRTLVTLEQSRARLIPIIVLLLQKAWRGTLARWRCRRLRAIYTIMRWFRRHKVRAHLAELQRRFQAARQPPLYGRDLVWPLPPAVLQPFQDTCHALFCRWRARQLVKNIPPSDMPQIKAKVAAMGALQGLRQDWGCRRAWARDYLSSATDNPTASSLFAQRLKTLQDKDGFGAVLFSSHVRKVNRFHKIRNRALLLTDQHLYKLDPDRQYRVMRAVPLEAVTGLSVTSGGDQLVVLHARGQDDLVVCLHRSRPPLDNRVGELVGVLAAHCQGEGRTLEVRVSDCIPLSHRGVRRLISVEPRPEQPEPDFRCARGSFTLLWPSR,PAAAAIQRHYNDEDPEKEKRIKELELLLMSTENELKGQQVLPTQNHTCSYPGW

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  

> open "/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"

Chain information for
MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Drag select of 184 residues  

> delete atoms sel

> delete bonds sel

Drag select of 86 residues  

> delete atoms sel

> delete bonds sel

Drag select of 60 residues  

> delete atoms sel

> delete bonds sel

Drag select of 2 residues  

> delete atoms sel

> delete bonds sel

> select clear

> ui tool show "Side View"

Drag select of 58 residues  

> delete atoms sel

> delete bonds sel

Drag select of 82 residues, 2 pseudobonds  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

Drag select of 18 residues, 1 pseudobonds  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

Drag select of 10 residues, 1 pseudobonds  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

Drag select of 7 residues  

> delete atoms sel

> delete bonds sel

> color bypolymer

> set bgColor white

> lighting flat

> view

Drag select of 1 pseudobonds  
No visible atoms or bonds selected  

> hide cartoons

> show cartoons

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "/Users/jrutter/Dropbox (MIT)/Ebert
> Lab/Ebert_computational/Alphafold
> screen/remote_job_0000742_longley/MYB_HUMAN__KIFC1_HUMAN__1313aa_scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json"

> alphafold pae #1 colorDomains true

> color bfactor #1 palette alphafold

6401 atoms, 806 residues, atom bfactor range 14.9 to 97.4  
Drag select of 6 residues, 1 pseudobonds  
Drag select of 37 residues  

> delete atoms sel

> delete bonds sel

Drag select of 10 residues, 1 pseudobonds  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

Drag select of 7 residues  

> delete atoms sel

> delete bonds sel

> select clear

Drag select of 12 residues, 1 pseudobonds  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

Drag select of 2 residues  

> delete atoms sel

> delete bonds sel

> hide cartoons

> show cartoons

> save "/Users/jrutter/Dropbox (MIT)/MYB_KIFC1_cleanup.cxs"

> show surfaces

> rainbow

> color bypolymer

Drag select of
MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A
SES surface, 2942 of 235002 triangles  
Drag select of
MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A
SES surface, 2958 of 235002 triangles  
[Repeated 1 time(s)]

> select clear

Drag select of
MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A
SES surface, 2958 of 235002 triangles  

> hide surfaces

> show surfaces

> transparency #1.2 70

Drag select of
MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B
SES surface, 57189 of 580510 triangles, 67 residues  

> transparency (#!1 & sel) 70

Drag select of
MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A
SES surface,
MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B
SES surface, 735 residues  

> transparency (#!1 & sel) 70

> ui tool show "AlphaFold Error Plot"

> color bfactor #1 palette alphafold

5865 atoms, 738 residues, 2 surfaces, atom bfactor range 14.9 to 97.4  

> transparency (#!1 & sel) 60

Drag select of
MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A
SES surface, 6498 of 235002 triangles,
MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B
SES surface, 9033 of 580510 triangles, 17 residues  

> color #1/B:163-198 lime

> color #1/B:240-673 magenta

> color #1/A:56-86 lime

> color #1/B:290-673 magenta

> color bfactor #1 palette alphafold

5865 atoms, 738 residues, 2 surfaces, atom bfactor range 14.9 to 97.4  

> color #1/A:54-78 lime

> color #1/B:306-673 magenta

> alphafold contacts #1/A toResidues #1/B

> transparency (#!1 & sel) 60

> color bfactor #1 palette alphafold

5865 atoms, 738 residues, 2 surfaces, atom bfactor range 14.9 to 97.4  

> select all

5865 atoms, 5959 bonds, 28 pseudobonds, 738 residues, 3 models selected  

> color bfactor #1 palette alphafold

5865 atoms, 738 residues, 2 surfaces, atom bfactor range 14.9 to 97.4  

> transparency (#!1 & sel) 60

> alphafold contacts #1/A toResidues #1/B distance 4

> alphafold contacts #1/A toResidues #1/B distance 4 color pLDDT

Expected a keyword  

> color bfactor #1 palette alphafold

5865 atoms, 738 residues, 2 surfaces, atom bfactor range 14.9 to 97.4  

> transparency (#!1 & sel) 60

> save "/Users/jrutter/Dropbox (MIT)/MYB_KIFC1_cleanup.cxs"

——— End of log from Sat Jul 22 22:07:52 2023 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2 Max
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: Mac14,5
      Model Number: MPHK3LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0 (22A8380)
      Kernel Version: Darwin 22.1.0
      Time since boot: 13 days, 6 hours, 46 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U3415W:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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, 2 years ago

Component: Unassigned → UI
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash deleting tool

comment:2 by Eric Pettersen, 2 years ago

Resolution: → can't reproduce
Status: accepted → closed
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