﻿id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14921	Crash in python_instances_of_class	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-13.0-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403271703 (2024-03-27 17:03:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x00000002badfb000 (most recent call first):
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00000001ffaba500 (most recent call first):
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 44 in python_instances_of_class
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 176 in _copy_custom_attrs
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 162 in copy
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 73 in assign_charges
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 102 in cmd_coulombic
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2904 in run
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run
  File ""/Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5F726.py"", line 62 in 
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py"", line 72 in _exec_python
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py"", line 95 in open_python_script
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py"", line 49 in runscript
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2904 in run
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 280 in event_loop
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init
  File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mlp._mlp, chimerax.coulombic._esp (total: 60)


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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5F726-F1-model_v4.pdb

AF-Q5F726-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for multidrug transporter (Q5F726) [more
info...]  
  
Chain information for AF-Q5F726-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | multidrug transporter | Q5F726_NEIG1 1-467  
  

> open /Users/diyamathai/Desktop/BIOL694/Group3_Project/SWISSMODEL_Q5F726.pdb

SWISSMODEL_Q5F726.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for SWISSMODEL_Q5F726.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker SWISSMODEL_Q5F726.pdb, chain A (#2) with AF-Q5F726-F1-model_v4.pdb,
chain A (#1), sequence alignment score = 2207.1  
RMSD between 411 pruned atom pairs is 0.711 angstroms; (across all 445 pairs:
1.403)  
  

> close session

> runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5F726.py

> open 1ADU

1adu title:  
Early E2A DNA-binding protein [more info...]  
  
Chain information for 1adu #1  
---  
Chain | Description | UniProt  
A B | ADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN | DNB2_ADE05 174-529  
  
Non-standard residues in 1adu #1  
---  
ZN — zinc ion  
  

> close session

> runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5F726.py

> open
> /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5F726-F1-model_v4.pdb

AF-Q5F726-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for multidrug transporter (Q5F726) [more
info...]  
  
Chain information for AF-Q5F726-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | multidrug transporter | Q5F726_NEIG1 1-467  
  

> show atoms

> hbonds reveal true

457 hydrogen bonds found  

> ~hbonds

Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> interfaces ~solvent

0 buried areas:  

> hide atoms

> color byhetero

> mlp

Map values for surface ""AF-Q5F726-F1-model_v4.pdb_A SES surface"": minimum
-27.22, mean -4.035, maximum 23.12  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-Q5F726-F1-model_v4.pdb_A SES surface #1.1: minimum,
-25.58, mean -0.11, maximum 13.39  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide surfaces

> color bfactor

3555 atoms, 467 residues, 1 surfaces, atom bfactor range 30.3 to 98.8  

> mlp

Map values for surface ""AF-Q5F726-F1-model_v4.pdb_A SES surface"": minimum
-27.22, mean -4.035, maximum 23.12  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide surfaces

> mlp

Map values for surface ""AF-Q5F726-F1-model_v4.pdb_A SES surface"": minimum
-27.22, mean -4.035, maximum 23.12  

> coulombic

Coulombic values for AF-Q5F726-F1-model_v4.pdb_A SES surface #1.1: minimum,
-25.58, mean -0.11, maximum 13.39  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide surfaces

> color #1 #d7caa8ff

> color #1 #d7ccafff

> show surfaces

> coulombic

Coulombic values for AF-Q5F726-F1-model_v4.pdb_A SES surface #1.1: minimum,
-25.58, mean -0.11, maximum 13.39  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface ""AF-Q5F726-F1-model_v4.pdb_A SES surface"": minimum
-27.22, mean -4.035, maximum 23.12  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Coulombic values for AF-Q5F726-F1-model_v4.pdb_A SES surface #1.1: minimum,
-25.58, mean -0.11, maximum 13.39  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface ""AF-Q5F726-F1-model_v4.pdb_A SES surface"": minimum
-27.22, mean -4.035, maximum 23.12  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide surfaces

> open /Users/diyamathai/Desktop/BIOL694/Group3_Project/SWISSMODEL_Q5F726.pdb

SWISSMODEL_Q5F726.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for SWISSMODEL_Q5F726.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker SWISSMODEL_Q5F726.pdb, chain A (#2) with AF-Q5F726-F1-model_v4.pdb,
chain A (#1), sequence alignment score = 2207.1  
RMSD between 411 pruned atom pairs is 0.711 angstroms; (across all 445 pairs:
1.403)  
  

> hide #1

> delete #1

> mlp

Map values for surface ""SWISSMODEL_Q5F726.pdb_A SES surface"": minimum -27.89,
mean -4.024, maximum 21.81  
Map values for surface ""SWISSMODEL_Q5F726.pdb_B SES surface"": minimum -27.09,
mean -4.004, maximum 22.34  
Map values for surface ""SWISSMODEL_Q5F726.pdb_C SES surface"": minimum -27.42,
mean -4, maximum 22.35  

> coulmbic

Unknown command: coulmbic  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for SWISSMODEL_Q5F726.pdb_A SES surface #2.1: minimum,
-14.34, mean -0.17, maximum 14.09  
Coulombic values for SWISSMODEL_Q5F726.pdb_B SES surface #2.2: minimum,
-13.89, mean -0.17, maximum 13.85  
Coulombic values for SWISSMODEL_Q5F726.pdb_C SES surface #2.3: minimum,
-14.08, mean -0.17, maximum 13.48  

> hide surfaces

> show atoms

> hide atoms

> color bfactor

10209 atoms, 1335 residues, 3 surfaces, atom bfactor range 0.61 to 0.97  

> color #2 #82d2ecff

> rainbow

> color byhetero

> show surfaces

> color byhetero

> coulombic

Coulombic values for SWISSMODEL_Q5F726.pdb_A SES surface #2.1: minimum,
-14.34, mean -0.17, maximum 14.09  
Coulombic values for SWISSMODEL_Q5F726.pdb_B SES surface #2.2: minimum,
-13.89, mean -0.17, maximum 13.85  
Coulombic values for SWISSMODEL_Q5F726.pdb_C SES surface #2.3: minimum,
-14.08, mean -0.17, maximum 13.48  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide surfaces

> color bypolymer

> select #2/A:21-465

3403 atoms, 3456 bonds, 445 residues, 1 model selected  

> select #2/B:21-465

3403 atoms, 3456 bonds, 445 residues, 1 model selected  

> select #2/C:21-465

3403 atoms, 3456 bonds, 445 residues, 1 model selected  

> style sel stick

Changed 3403 atom styles  

> style sel sphere

Changed 3403 atom styles  

> style sel ball

Changed 3403 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> hide sel surfaces

> hide sel cartoons

> show sel cartoons

> clear sel

Unknown command: clear sel  

> select clear

> hide cartoons

> show cartoons

> show atoms

> hide cartoons

> show cartoons

> hide atoms

> show surfaces

> hide surfaces

> show atoms

> hide cartoons

> style stick

Changed 10209 atom styles  

> style stick

Changed 10209 atom styles  

> style sphere

Changed 10209 atom styles  

> style ball

Changed 10209 atom styles  

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> show cartoons

> hide atoms

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides ladder

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> close session

> open /Users/diyamathai/Desktop/BIOL694/Group3_Project/SWISSMODEL_Q5F726.pdb

SWISSMODEL_Q5F726.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for SWISSMODEL_Q5F726.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/diyamathai/Desktop/movie1.mp4

Movie saved to /Users/diyamathai/Desktop/movie1.mp4  
  

> close session

> runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5F726.py

> open
> /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5F726-F1-model_v4.pdb

AF-Q5F726-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for multidrug transporter (Q5F726) [more
info...]  
  
Chain information for AF-Q5F726-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | multidrug transporter | Q5F726_NEIG1 1-467  
  

> movie record

> turn y 2 180

> wait 180

> mlp

Map values for surface ""AF-Q5F726-F1-model_v4.pdb_A SES surface"": minimum
-27.22, mean -4.035, maximum 23.12  

> turn y 2 180

> wait 180

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-Q5F726-F1-model_v4.pdb_A SES surface #1.1: minimum,
-25.58, mean -0.11, maximum 13.39  

> turn y 2 180

> wait 180

> hide surfaces

> open /Users/diyamathai/Desktop/BIOL694/Group3_Project/SWISSMODEL_Q5F726.pdb

SWISSMODEL_Q5F726.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for SWISSMODEL_Q5F726.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker SWISSMODEL_Q5F726.pdb, chain A (#2) with AF-Q5F726-F1-model_v4.pdb,
chain A (#1), sequence alignment score = 2207.1  
RMSD between 411 pruned atom pairs is 0.711 angstroms; (across all 445 pairs:
1.403)  
  

> turn y 2 180

> wait 180

> delete #1

> mlp

Map values for surface ""SWISSMODEL_Q5F726.pdb_A SES surface"": minimum -27.89,
mean -4.024, maximum 21.81  
Map values for surface ""SWISSMODEL_Q5F726.pdb_B SES surface"": minimum -27.09,
mean -4.004, maximum 22.34  
Map values for surface ""SWISSMODEL_Q5F726.pdb_C SES surface"": minimum -27.42,
mean -4, maximum 22.35  

> turn y 2 180

> wait 180

> coulombic


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: MYD82LL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0 (22A380)
      Kernel Version: Darwin 22.1.0
      Time since boot: 38 days, 15 hours, 15 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.1.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202403271703
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    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-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

}}}
"	defect	closed	normal		Core		duplicate		Tom Goddard				all	ChimeraX
