Crash in event loop

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-60-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.9rc202410290434 (2024-10-29 04:34:53 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000079cddcff9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000079ce35848b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, 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 (total: 55)
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202410290434 (2024-10-29)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 0_10_chl_model.cif

Summary of feedback from opening 0_10_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_10_chl_model.cif #1  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

Computing secondary structure  

> open 0_1_chl_model.cif

Summary of feedback from opening 0_1_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_1_chl_model.cif #2  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_2_chl_model.cif

Summary of feedback from opening 0_2_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_2_chl_model.cif #3  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_3_chl_model.cif

Summary of feedback from opening 0_3_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_3_chl_model.cif #4  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_4_chl_model.cif

Summary of feedback from opening 0_4_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_4_chl_model.cif #5  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_5_chl_model.cif

Summary of feedback from opening 0_5_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_5_chl_model.cif #6  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_6_chl_model.cif

Summary of feedback from opening 0_6_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_6_chl_model.cif #7  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_7_chl_model.cif

Summary of feedback from opening 0_7_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_7_chl_model.cif #8  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_8_chl_model.cif

Summary of feedback from opening 0_8_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_8_chl_model.cif #9  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_9_chl_model.cif

Summary of feedback from opening 0_9_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_9_chl_model.cif #10  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

Computing secondary structure  

> select /B

460 atoms, 500 bonds, 40 pseudobonds, 10 residues, 20 models selected  

> select clear

> ui tool show Matchmaker

> matchmaker #!2-10 to #1

Computing secondary structure  
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 0_10_chl_model.cif, chain A (#1) with 0_1_chl_model.cif, chain A
(#2), sequence alignment score = 533.4  
RMSD between 94 pruned atom pairs is 0.957 angstroms; (across all 135 pairs:
2.009)  
  
Matchmaker 0_10_chl_model.cif, chain A (#1) with 0_2_chl_model.cif, chain A
(#3), sequence alignment score = 530  
RMSD between 100 pruned atom pairs is 0.834 angstroms; (across all 135 pairs:
1.991)  
  
Matchmaker 0_10_chl_model.cif, chain A (#1) with 0_3_chl_model.cif, chain A
(#4), sequence alignment score = 535.4  
RMSD between 97 pruned atom pairs is 0.722 angstroms; (across all 135 pairs:
2.479)  
  
Matchmaker 0_10_chl_model.cif, chain A (#1) with 0_4_chl_model.cif, chain A
(#5), sequence alignment score = 545.7  
RMSD between 90 pruned atom pairs is 0.818 angstroms; (across all 135 pairs:
2.530)  
  
Matchmaker 0_10_chl_model.cif, chain A (#1) with 0_5_chl_model.cif, chain A
(#6), sequence alignment score = 535.4  
RMSD between 99 pruned atom pairs is 0.960 angstroms; (across all 135 pairs:
2.840)  
  
Matchmaker 0_10_chl_model.cif, chain A (#1) with 0_6_chl_model.cif, chain A
(#7), sequence alignment score = 534.8  
RMSD between 109 pruned atom pairs is 0.797 angstroms; (across all 135 pairs:
1.754)  
  
Matchmaker 0_10_chl_model.cif, chain A (#1) with 0_7_chl_model.cif, chain A
(#8), sequence alignment score = 562.1  
RMSD between 95 pruned atom pairs is 0.750 angstroms; (across all 135 pairs:
2.556)  
  
Matchmaker 0_10_chl_model.cif, chain A (#1) with 0_8_chl_model.cif, chain A
(#9), sequence alignment score = 520.9  
RMSD between 100 pruned atom pairs is 0.849 angstroms; (across all 135 pairs:
2.765)  
  
Matchmaker 0_10_chl_model.cif, chain A (#1) with 0_9_chl_model.cif, chain A
(#10), sequence alignment score = 553.1  
RMSD between 108 pruned atom pairs is 0.766 angstroms; (across all 135 pairs:
1.953)  
  

> view clip false

> select /B

460 atoms, 500 bonds, 40 pseudobonds, 10 residues, 20 models selected  

> ui tool show Clashes

> clashes sel restrict /A interModel false

9 clashes  

> ui tool show H-Bonds

> hbonds sel interModel false intraRes false reveal true

9 hydrogen bonds found  

> color sel byhetero

> color bfactor palette alphafold

10933 atoms, 1360 residues, atom bfactor range 52.2 to 98.9  

> hide #!10 models

> hide #!9 models

> hide #!7 models

> hide #!8 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> select clear

> color #!1 byhetero

> mlp #!1

Map values for surface "0_10_chl_model.cif_A SES surface": minimum -27.56,
mean -4.879, maximum 22.23  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!1 models

> show #!2 models

> show #!3 models

> hide #!2 models

> color #!3 byhetero

> mlp #!3

Map values for surface "0_2_chl_model.cif_A SES surface": minimum -25.3, mean
-4.805, maximum 26.09  
To also show corresponding color key, enter the above mlp command and add key
true  

> surface hidePatches #3,11

> mlp #!3

Map values for surface "0_2_chl_model.cif_A SES surface": minimum -25.3, mean
-4.805, maximum 26.09  
To also show corresponding color key, enter the above mlp command and add key
true  

> show #!4 models

> hide #!3 models

> color #!4 byhetero


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202410290434 (2024-10-29)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 0_10_chl_model.cif

Summary of feedback from opening 0_10_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_10_chl_model.cif #1  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

Computing secondary structure  

> open 0_1_chl_model.cif

Summary of feedback from opening 0_1_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_1_chl_model.cif #2  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_2_chl_model.cif

Summary of feedback from opening 0_2_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_2_chl_model.cif #3  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_3_chl_model.cif

Summary of feedback from opening 0_3_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_3_chl_model.cif #4  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_4_chl_model.cif

Summary of feedback from opening 0_4_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_4_chl_model.cif #5  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_5_chl_model.cif

Summary of feedback from opening 0_5_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_5_chl_model.cif #6  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_6_chl_model.cif

Summary of feedback from opening 0_6_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_6_chl_model.cif #7  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_7_chl_model.cif

Summary of feedback from opening 0_7_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_7_chl_model.cif #8  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_8_chl_model.cif

Summary of feedback from opening 0_8_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_8_chl_model.cif #9  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> open 0_9_chl_model.cif

Summary of feedback from opening 0_9_chl_model.cif  
---  
warning | Unable to fetch template for 'CHL-IDE': will connect using distance criteria  
  
Chain information for 0_9_chl_model.cif #10  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

Computing secondary structure  
[Repeated 8 time(s)]




OpenGL version: 3.3.0 NVIDIA 570.133.20
OpenGL renderer: NVIDIA GeForce RTX 4070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_IL.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision Tower 7910
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 48 Intel(R) Xeon(R) CPU E5-2670 v3 @ 2.30GHz
Cache Size: 30720 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           125Gi       3.3Gi       722Mi       481Mi       121Gi       121Gi
	Swap:          2.0Gi       177Mi       1.8Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2782] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:e130]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202410290434
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.5
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2
    ChimeraX-Label: 1.1.11
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.17
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.2.2
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    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: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.7
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    joblib: 1.5.1
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    llvmlite: 0.44.0
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.3
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    msgpack: 1.0.8
    narwhals: 1.41.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numba: 0.61.2
    numexpr: 2.10.1
    numpy: 2.2.6
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 6.0.1
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.8.1
    pynmrstar: 3.3.4
    pynndescent: 0.5.13
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scikit-learn: 1.6.1
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    threadpoolctl: 3.6.0
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomlkit: 0.13.2
    tornado: 6.4.1
    tqdm: 4.67.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    umap-learn: 0.5.7
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13