Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-26-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x000076b7d82c5b80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 69 in residue_or_none
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 71 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 71 in residues_or_nones
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 177 in get_prop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1159 in _get_numbering_start
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 866 in __copy__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1130 in __copy__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/copy.py", line 84 in copy
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 117 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/seqalign/manager.py", line 253 in new_alignment
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 241 in seqalign_chain
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/show_sequences/tool.py", line 77 in show_seqs
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, 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 (total: 59)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/em313/Documents/ATP-Vi-HF380/1388-1694.pdb

Chain information for 1388-1694.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /home/em313/Documents/ATP-Vi-
> HF380/J50-2-30A-resolution/J50_007_volume_map_sharp_1mol.mrc
> /home/em313/Documents/ATP-Vi-HF380/J50-2-30A-resolution/strut_ver2.pdb
> /home/em313/Documents/ATP-Vi-HF380/J50-2-30A-resolution/1059-1146_ver2.pdb
> /home/em313/Documents/ATP-Vi-HF380/J50-2-30A-resolution/1388-1694.pdb
> /home/em313/Documents/ATP-Vi-HF380/J50-2-30A-resolution/1388-1694_ver2.pdb

Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/J50-2-30A-resolution/strut_ver2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A
1060 ASN A 1073 1 14  
Start residue of secondary structure not found: HELIX 2 2 PRO A 1078 GLN A
1097 1 20  
Start residue of secondary structure not found: HELIX 3 3 THR A 1098 ILE A
1100 1 3  
Start residue of secondary structure not found: HELIX 4 4 ALA A 1127 ILE A
1139 1 13  
Start residue of secondary structure not found: HELIX 5 5 SER A 1140 PHE A
1143 1 4  
120 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 130 130 ASN A 3887 MET A
3900 1 14  
Start residue of secondary structure not found: HELIX 131 131 GLU A 3901 GLN A
3905 1 5  
Start residue of secondary structure not found: HELIX 132 132 LEU A 3913 ASN A
3925 1 13  
Start residue of secondary structure not found: HELIX 133 133 PRO A 3928 LEU A
3930 1 3  
Start residue of secondary structure not found: HELIX 134 134 PRO A 3936 VAL A
3955 1 20  
Start residue of secondary structure not found: HELIX 135 135 THR A 3956 THR A
3958 1 3  
87 messages similar to the above omitted  
  
Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/J50-2-30A-resolution/1059-1146_ver2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 6 6 LEU A
1148 ASP A 1155 1 8  
Start residue of secondary structure not found: HELIX 7 7 ALA A 1156 GLN A
1158 1 3  
Start residue of secondary structure not found: HELIX 8 8 ARG A 1167 LEU A
1191 1 25  
Start residue of secondary structure not found: HELIX 9 9 PRO A 1199 GLY A
1219 1 21  
Start residue of secondary structure not found: HELIX 10 10 LEU A 1224 ILE A
1237 1 14  
212 messages similar to the above omitted  
  
Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/J50-2-30A-resolution/1388-1694.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A
1060 ASN A 1073 1 14  
Start residue of secondary structure not found: HELIX 2 2 PRO A 1078 GLN A
1097 1 20  
Start residue of secondary structure not found: HELIX 3 3 THR A 1098 ILE A
1100 1 3  
Start residue of secondary structure not found: HELIX 4 4 ALA A 1127 ILE A
1139 1 13  
Start residue of secondary structure not found: HELIX 5 5 SER A 1140 PHE A
1143 1 4  
202 messages similar to the above omitted  
  
Opened J50_007_volume_map_sharp_1mol.mrc as #2, grid size 600,600,600, pixel
0.873, shown at level 0.0679, step 4, values float32  
Chain information for strut_ver2.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for 1059-1146_ver2.pdb #4  
---  
Chain | Description  
A | No description available  
  
Chain information for 1388-1694.pdb #5  
---  
Chain | Description  
A | No description available  
  
Chain information for 1388-1694_ver2.pdb #6  
---  
Chain | Description  
A | No description available  
  

> open /home/em313/Documents/ATP-Vi-HF380/ATPVimodel001-coot-0.pdb
> /home/em313/Documents/ATP-Vi-HF380/1388-1694.pdb

Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/ATPVimodel001-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TRP A 171
ALA A 187 1 17  
Start residue of secondary structure not found: HELIX 2 2 MET A 188 MET A 190
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 195 PHE A 197
1 3  
Start residue of secondary structure not found: HELIX 4 4 GLU A 199 GLY A 234
1 36  
Start residue of secondary structure not found: HELIX 5 5 GLY A 236 LEU A 241
1 6  
25 messages similar to the above omitted  
PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for ATPVimodel001-coot-0.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for 1388-1694.pdb #8  
---  
Chain | Description  
A | No description available  
  

> open "/home/em313/Documents/ATP-Vi-HF380/J50_007_volume_map_sharp_1mol
> ver3.pdb"

Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/J50_007_volume_map_sharp_1mol ver3.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 6 6 LEU A
1148 ASP A 1155 1 8  
Start residue of secondary structure not found: HELIX 7 7 ALA A 1156 GLN A
1158 1 3  
Start residue of secondary structure not found: HELIX 8 8 ARG A 1167 LEU A
1191 1 25  
Start residue of secondary structure not found: HELIX 9 9 PRO A 1199 GLY A
1219 1 21  
Start residue of secondary structure not found: HELIX 10 10 LEU A 1224 ILE A
1237 1 14  
833 messages similar to the above omitted  
  
Chain information for J50_007_volume_map_sharp_1mol ver3.pdb  
---  
Chain | Description  
9.1/A | No description available  
9.2/A | No description available  
9.3/A 9.4/A 9.5/A | No description available  
9.1/B | No description available  
  

> close #2

> hide #!8 models

> hide #!7 models

> hide #!9.1 models

> hide #9.2 models

> hide #!9.3 models

> hide #!9.4 models

> hide #!9.5 models

> hide #!9 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> show #!8 models

> hide #!7 models

> view

> hide #!8 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #3 models

> hide #4 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> close #1

> ui tool show Matchmaker

> matchmaker #!6 to #5

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 1388-1694.pdb, chain A (#5) with 1388-1694_ver2.pdb, chain A (#6),
sequence alignment score = 1068.1  
RMSD between 205 pruned atom pairs is 0.000 angstroms; (across all 205 pairs:
0.000)  
  

> hide #!8 models

> show #!8 models

> close #5

> matchmaker #!6 to #8

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 1388-1694.pdb, chain A (#8) with 1388-1694_ver2.pdb, chain A (#6),
sequence alignment score = 1068.1  
RMSD between 205 pruned atom pairs is 0.000 angstroms; (across all 205 pairs:
0.000)  
  

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> matchmaker #!6 to #8

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 1388-1694.pdb, chain A (#8) with 1388-1694_ver2.pdb, chain A (#6),
sequence alignment score = 1068.1  
RMSD between 205 pruned atom pairs is 0.000 angstroms; (across all 205 pairs:
0.000)  
  

> close #6

> show #!9 models

> show #!9.1 models

> open /home/em313/Documents/ATP-Vi-HF380/1388-1694.pdb

Chain information for 1388-1694.pdb #1  
---  
Chain | Description  
A | No description available  
  

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> close #8

> close #9

> open "/home/em313/Documents/ATP-Vi-HF380/J50_007_volume_map_sharp_1mol
> ver3.pdb"

Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/J50_007_volume_map_sharp_1mol ver3.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 6 6 LEU A
1148 ASP A 1155 1 8  
Start residue of secondary structure not found: HELIX 7 7 ALA A 1156 GLN A
1158 1 3  
Start residue of secondary structure not found: HELIX 8 8 ARG A 1167 LEU A
1191 1 25  
Start residue of secondary structure not found: HELIX 9 9 PRO A 1199 GLY A
1219 1 21  
Start residue of secondary structure not found: HELIX 10 10 LEU A 1224 ILE A
1237 1 14  
833 messages similar to the above omitted  
  
Chain information for J50_007_volume_map_sharp_1mol ver3.pdb  
---  
Chain | Description  
2.1/A | No description available  
2.2/A | No description available  
2.3/A 2.4/A 2.5/A | No description available  
2.1/B | No description available  
  

> close #2

> open /home/em313/Documents/ATP-Vi-HF380/ATPVimodel001-coot-0.pdb

Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/ATPVimodel001-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TRP A 171
ALA A 187 1 17  
Start residue of secondary structure not found: HELIX 2 2 MET A 188 MET A 190
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 195 PHE A 197
1 3  
Start residue of secondary structure not found: HELIX 4 4 GLU A 199 GLY A 234
1 36  
Start residue of secondary structure not found: HELIX 5 5 GLY A 236 LEU A 241
1 6  
25 messages similar to the above omitted  
PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for ATPVimodel001-coot-0.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open "/home/em313/Documents/ATP-Vi-
> HF380/J50-2-30A-resolution/J50_007_volume_map_sharp_1mol ver2.mrc"

Opened J50_007_volume_map_sharp_1mol ver2.mrc as #5, grid size 600,600,600,
pixel 0.873, shown at level 0.00423, step 4, values float32  

> volume #5 step 1

> ui mousemode right "map eraser"

> volume erase #5 center 177.77,63.192,281.87 radius 135.73

Opened J50_007_volume_map_sharp_1mol ver2.mrc copy as #8, grid size
600,600,600, pixel 0.873, shown at step 1, values float32  

> volume erase #8 center 358.22,70.834,166.32 radius 135.66

> volume erase #8 center 294.18,53.522,367.41 radius 135.66

> volume erase #8 center 134.33,162.3,146.52 radius 135.66

> volume erase #8 center 295.36,61.017,235.46 radius 135.66

> select add #8

2 models selected  

> color #8 #ffbe6fff models

> transparency #8.1 50

> volume erase #8 center 319.02,229.59,212.29 radius 45.047

> volume erase #8 center 217.87,309.93,239.96 radius 37.714

> volume erase #8 center 276,264.56,203.2 radius 37.714

> volume erase #8 center 281.61,319.08,220.41 radius 37.714

> hide #6 models

> save "/home/em313/Documents/ATP-Vi-
> HF380/J50-2-30A-resolution/J50_007_volume_map_sharp_1mol ver3.mrc" models #8

> show #!7 models

> close #2

> hide #!8 models

> select subtract #8

Nothing selected  

> hide #!1 models

> show #!1 models

> delete #1 /A:1388-1441

> save /home/em313/Documents/ATP-Vi-HF380/1694.pdb models #1

> ui tool show "Show Sequence Viewer"

> sequence chain #7/A

Alignment identifier is 7/A  

> select #7 /A:1388-1441

425 atoms, 442 bonds, 54 residues, 1 model selected  

> select #7 /A:1000-1441

3065 atoms, 3147 bonds, 1 pseudobond, 381 residues, 2 models selected  

> save /home/em313/Documents/ATP-Vi-HF380/ATPVimodel001-coot-0.fasta format
> fasta alignment 7/A

> close #7

> open /home/em313/Documents/ATP-Vi-HF380/ATPVimodel001-coot-1.pdb

Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/ATPVimodel001-coot-1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TRP A 171
ALA A 187 1 17  
Start residue of secondary structure not found: HELIX 2 2 MET A 188 MET A 190
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 195 PHE A 197
1 3  
Start residue of secondary structure not found: HELIX 4 4 GLU A 199 GLY A 234
1 36  
Start residue of secondary structure not found: HELIX 5 5 GLY A 236 LEU A 241
1 6  
25 messages similar to the above omitted  
PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for ATPVimodel001-coot-1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 535.161.07
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 7 5700X 8-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           125Gi       3.7Gi       114Gi        42Mi       7.5Gi       120Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	0f:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1)	
	Subsystem: ZOTAC International (MCO) Ltd. TU102 [GeForce RTX 2080 Ti] [19da:2503]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.10.5
    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: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    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: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    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
    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-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.2
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.3
    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: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    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: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    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: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9