Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.14.0-70.13.1.el9_0.x86_64-x86_64-with-glibc2.34
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

Thread 0x00007f4f6d4bf640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 324 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 622 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1392 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f4fde7fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 324 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 622 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1392 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007f5037635b80 (most recent call first):
  Garbage-collecting
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/ctypes/__init__.py", line 512 in cast
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/numpy/core/_internal.py", line 282 in data_as
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 208 in get_prop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/std_commands/delete.py", line 48 in delete_atoms
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1310 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/libexec/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.map._map, chimerax.surface._surface, 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, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 54)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> functionkey F4 view orient

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 /run/media/admin/_data/lab-
> data/ananya/D14-D25-SO2/Jan2025/combined-5FOLD-4Amap-9thJan-onlyE.pdb
> /run/media/admin/_data/lab-
> data/ananya/D14-D25-SO2/Jan2025/combination5foldonly-7kv8.pdb

Chain information for combined-5FOLD-4Amap-9thJan-onlyE.pdb #1  
---  
Chain | Description  
G I Q S a c k m u w | No description available  
H J R T b d l n v x | No description available  
  
Chain information for combination5foldonly-7kv8.pdb #2  
---  
Chain | Description  
A B C D E F G H I J | No description available  
K L M N b | No description available  
O P Q R c | No description available  
  

> hide atoms

> show cartoons

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/B:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/C:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/D:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/E:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/F:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/G:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/H:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/I:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/J:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #1/G:1-495

3805 atoms, 3884 bonds, 495 residues, 1 model selected  

> select #1/I:1-495

3805 atoms, 3884 bonds, 495 residues, 1 model selected  

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/B:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/C:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/D:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/E:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/F:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/I:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/J:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/O:90-164

589 atoms, 605 bonds, 75 residues, 1 model selected  

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/B:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/P:90-164

589 atoms, 605 bonds, 75 residues, 1 model selected  

> select #2/O:90-164

589 atoms, 605 bonds, 75 residues, 1 model selected  

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/O:90-164

589 atoms, 605 bonds, 75 residues, 1 model selected  

> select #2/A:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/G:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/B:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/H:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/B:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/C:1-495

3773 atoms, 3851 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/D:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> select #2/E:1-495

3777 atoms, 3855 bonds, 1 pseudobond, 493 residues, 2 models selected  

> ui tool show Matchmaker

> select #1/a:1-495

3805 atoms, 3884 bonds, 495 residues, 1 model selected  

> matchmaker #1/G#1/I#1/Q#1/S#1/a#1/c#1/k#1/m#1/u#1/w to
> #2/A#2/B#2/C#2/D#2/E#2/F#2/G#2/H#2/I#2/J pairing ss

Parameters  
---  
Chain pairing | ss  
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 combination5foldonly-7kv8.pdb, chain A (#2) with
combined-5FOLD-4Amap-9thJan-onlyE.pdb, chain G (#1), sequence alignment score
= 2404.7  
Matchmaker combination5foldonly-7kv8.pdb, chain B (#2) with
combined-5FOLD-4Amap-9thJan-onlyE.pdb, chain I (#1), sequence alignment score
= 2404.7  
Matchmaker combination5foldonly-7kv8.pdb, chain C (#2) with
combined-5FOLD-4Amap-9thJan-onlyE.pdb, chain Q (#1), sequence alignment score
= 2413.1  
Matchmaker combination5foldonly-7kv8.pdb, chain D (#2) with
combined-5FOLD-4Amap-9thJan-onlyE.pdb, chain S (#1), sequence alignment score
= 2404.7  
Matchmaker combination5foldonly-7kv8.pdb, chain E (#2) with
combined-5FOLD-4Amap-9thJan-onlyE.pdb, chain a (#1), sequence alignment score
= 2404.7  
Matchmaker combination5foldonly-7kv8.pdb, chain F (#2) with
combined-5FOLD-4Amap-9thJan-onlyE.pdb, chain c (#1), sequence alignment score
= 2404.7  
Matchmaker combination5foldonly-7kv8.pdb, chain G (#2) with
combined-5FOLD-4Amap-9thJan-onlyE.pdb, chain k (#1), sequence alignment score
= 2413.1  
Matchmaker combination5foldonly-7kv8.pdb, chain H (#2) with
combined-5FOLD-4Amap-9thJan-onlyE.pdb, chain m (#1), sequence alignment score
= 2413.1  
Matchmaker combination5foldonly-7kv8.pdb, chain I (#2) with
combined-5FOLD-4Amap-9thJan-onlyE.pdb, chain u (#1), sequence alignment score
= 2413.1  
Matchmaker combination5foldonly-7kv8.pdb, chain J (#2) with
combined-5FOLD-4Amap-9thJan-onlyE.pdb, chain w (#1), sequence alignment score
= 2413.1  
RMSD between 454 pruned atom pairs is 1.065 angstroms; (across all 4930 pairs:
114.620)  
  

> select clear

> select add #1

43940 atoms, 44890 bonds, 5700 residues, 1 model selected  

> show sel surfaces

> select subtract #1

20 models selected  

> select add #2

45825 atoms, 45325 bonds, 10 pseudobonds, 7145 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #2

20 models selected  

> select add #1

43940 atoms, 44890 bonds, 5700 residues, 1 model selected  

> hide sel surfaces

> ui tool show "Change Chain IDs"

> hide #!2 models

> close #2

> select clear

> ui tool show "Change Chain IDs"

> ui tool show "Show Sequence Viewer"

> sequence chain /H /J /R /T /b /d /l /n /v /x

Alignment identifier is 1  

> select /H,J,R,T,b,d,l,n,v,x:75

80 atoms, 70 bonds, 10 residues, 1 model selected  

> select /H,J,R,T,b,d,l,n,v,x

5890 atoms, 6050 bonds, 750 residues, 1 model selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> ui tool show "Show Sequence Viewer"

> sequence chain /G /I /Q /S /a /c /k /m /u /w

Alignment identifier is 1  

> select /G-w:395-396

100 atoms, 90 bonds, 20 residues, 1 model selected  

> select /G-w:395-495

7430 atoms, 7560 bonds, 1010 residues, 1 model selected  

> delete atoms (#!1 & sel)


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> functionkey F4 view orient

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 550.54.14
OpenGL renderer: NVIDIA RTX A5000/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=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: GIGABYTE
Model: MU72-SU0-00
OS: Rocky Linux 9.3 Blue Onyx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 Intel(R) Xeon(R) Platinum 8352Y CPU @ 2.20GHz
Cache Size: 49152 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           502Gi       5.7Gi       497Gi        33Mi       1.7Gi       497Gi
	Swap:          127Gi          0B       127Gi

Graphics:
	06:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 52)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:1000]	
	Kernel driver in use: ast

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-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-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-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    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
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    line-profiler: 4.0.2
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    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
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    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
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    PyOpenGL-accelerate: 3.1.7
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    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
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    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
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    pytz: 2023.3.post1
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    QtPy: 2.4.1
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    requests: 2.31.0
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    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
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    tables: 3.8.0
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    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
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    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9