KeyError matching selected regions

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-26-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /home/pasquale/RAB29_comparison.cxs

Log from Tue Apr 2 13:16:34 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/pasquale/Scaricati/8fo9.pdb

8fo9.pdb title:  
Cryo-em structure of RAB29-LRRK2 complex In the LRRK2 tetramer state [more
info...]  
  
Chain information for 8fo9.pdb #1  
---  
Chain | Description | UniProt  
A C E F | dardarin | LRRK2_HUMAN 1-2527  
B D | ras-related protein rab-7L1 | RAB7L_HUMAN 1-177  
  
Non-standard residues in 8fo9.pdb #1  
---  
ATP — adenosine-5'-triphosphate  
GDP — guanosine-5'-diphosphate  
  

> ui tool show Registration

> hide atoms

> show cartoons

> open
> /home/pasquale/trantor/LRRK2/Saint/colabfold_models/best_models/O14966_RAB29.pdb

No such file/path:
/home/pasquale/trantor/LRRK2/Saint/colabfold_models/best_models/O14966_RAB29.pdb  

> open /home/pasquale/trantor/LRRK2/Saint/best_models/O14966_RAB29.pdb

Chain information for O14966_RAB29.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

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 8fo9.pdb, chain F (#1) with O14966_RAB29.pdb, chain A (#2),
sequence alignment score = 11600.8  
RMSD between 447 pruned atom pairs is 1.092 angstroms; (across all 2289 pairs:
62.153)  
  

> ui tool show Matchmaker

> matchmaker #2/B to #1/B 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 8fo9.pdb, chain B (#1) with O14966_RAB29.pdb, chain B (#2),
sequence alignment score = 833.2  
RMSD between 148 pruned atom pairs is 0.940 angstroms; (across all 165 pairs:
1.480)  
  

> hide #2 models

> show #2 models

> ui tool show Matchmaker

> matchmaker #2/A to #1/E 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 8fo9.pdb, chain E (#1) with O14966_RAB29.pdb, chain A (#2),
sequence alignment score = 11556.4  
RMSD between 447 pruned atom pairs is 1.093 angstroms; (across all 2287 pairs:
62.178)  
  

> ui tool show Matchmaker

> matchmaker #2/A to #1/F 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 8fo9.pdb, chain F (#1) with O14966_RAB29.pdb, chain A (#2),
sequence alignment score = 11600.8  
RMSD between 447 pruned atom pairs is 1.092 angstroms; (across all 2289 pairs:
62.153)  
  

> select #1/E

17049 atoms, 17349 bonds, 13 pseudobonds, 2289 residues, 2 models selected  

> select #1/C

8831 atoms, 9010 bonds, 4 pseudobonds, 1175 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2/A to #1/C 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 8fo9.pdb, chain C (#1) with O14966_RAB29.pdb, chain A (#2),
sequence alignment score = 10372.6  
RMSD between 604 pruned atom pairs is 1.246 angstroms; (across all 1173 pairs:
3.304)  
  

> select clear

> select #1/A#1/C#1/E#1/F

51631 atoms, 52590 bonds, 34 pseudobonds, 6930 residues, 2 models selected  

> hide sel cartoons

> select #1/B#1/D

2111 atoms, 2144 bonds, 2 pseudobonds, 331 residues, 2 models selected  

> hide sel cartoons

> select #1/C

8831 atoms, 9010 bonds, 4 pseudobonds, 1175 residues, 2 models selected  

> show sel cartoons

> select clear

Drag select of 328 residues, 1 pseudobonds  

> select clear

> open 7lih

Summary of feedback from opening 7lih fetched from pdb  
---  
note | Fetching compressed mmCIF 7lih from
http://files.rcsb.org/download/7lih.cif  
  
7lih title:  
CryoEM structure of Mayaro virus icosahedral subunit [more info...]  
  
Chain information for 7lih #3  
---  
Chain | Description | UniProt  
A B C F | Capsid protein | POLS_MAYAB 98-257  
D E G M | E2 protein | A0A0P0BWJ4_9VIRU 7-416  
H I J T | E1 protein | A0A0P0CE34_9VIRU 1-435  
  

> close #3

> open 7liw

Summary of feedback from opening 7liw fetched from pdb  
---  
notes | Fetching compressed mmCIF 7liw from
http://files.rcsb.org/download/7liw.cif  
Fetching CCD COA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/COA/COA.cif  
Fetching CCD Y2A from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/Y2A/Y2A.cif  
  
7liw title:  
Local refinement of human ATP citrate lyase E599Q mutant ASH domain [more
info...]  
  
Chain information for 7liw #3  
---  
Chain | Description | UniProt  
A B C D | ATP-citrate synthase | ACLY_HUMAN 1-1101  
  
Non-standard residues in 7liw #3  
---  
ADP — adenosine-5'-diphosphate  
COA — coenzyme A  
Y2A — (2S)-2-hydroxy-2-[2-oxo-2-(phosphonooxy)ethyl]butanedioic acid  
  

> close #3

> open 7lhw

7lhw title:  
Structure of the LRRK2 monomer [more info...]  
  
Chain information for 7lhw #3  
---  
Chain | Description | UniProt  
A | Leucine-rich repeat serine/threonine-protein kinase 2 | LRRK2_HUMAN 1-2527  
  
Non-standard residues in 7lhw #3  
---  
ATP — adenosine-5'-triphosphate  
GDP — guanosine-5'-diphosphate  
  

> ui tool show Matchmaker

> matchmaker #3/A to #2/A 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 O14966_RAB29.pdb, chain A (#2) with 7lhw, chain A (#3), sequence
alignment score = 10788.4  
RMSD between 460 pruned atom pairs is 1.035 angstroms; (across all 1813 pairs:
18.114)  
  

> save /home/pasquale/RAB29_comparison.cxs

——— End of log from Tue Apr 2 13:16:34 2024 ———

opened ChimeraX session  

> select #2/B

3218 atoms, 3249 bonds, 203 residues, 1 model selected  

> select #1/B#1/D

2111 atoms, 2144 bonds, 2 pseudobonds, 331 residues, 2 models selected  

> show sel cartoons

> select #1/A#1/C#1/E#1/F

51631 atoms, 52590 bonds, 34 pseudobonds, 6930 residues, 2 models selected  

> show sel cartoons

> hide #!3 models

> select clear

> ui tool show Matchmaker

> matchmaker #2/B to #1/B 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 8fo9.pdb, chain B (#1) with O14966_RAB29.pdb, chain B (#2),
sequence alignment score = 833.2  
RMSD between 148 pruned atom pairs is 0.940 angstroms; (across all 165 pairs:
1.480)  
  

> matchmaker #2/B to #1/B 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 8fo9.pdb, chain B (#1) with O14966_RAB29.pdb, chain B (#2),
sequence alignment score = 833.2  
RMSD between 148 pruned atom pairs is 0.940 angstroms; (across all 165 pairs:
1.480)  
  
Drag select of 8 residues  

> select clear

Drag select of 1670 residues, 6 pseudobonds  

> ui tool show Matchmaker

> matchmaker #1/E to #2/A 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 O14966_RAB29.pdb, chain A (#2) with 8fo9.pdb, chain E (#1),
sequence alignment score = 11556.4  
RMSD between 447 pruned atom pairs is 1.093 angstroms; (across all 2287 pairs:
62.178)  
  

> matchmaker #1/E & sel to #2/A & sel pairing ss

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 169, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 288, in run_matchmaker  
run(self.session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 730, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
KeyError: <chimerax.atomic.molobject.StructureSeq object at 0x7cab93629760>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
  
See log for complete Python traceback.  
  

> undo

[Repeated 8 time(s)]Drag select of 175 residues  

> select clear

> select

111771 atoms, 113439 bonds, 44 pseudobonds, 11806 residues, 5 models selected  

> show sel cartoons

> hide #!3 models

> select subtract #3

97465 atoms, 98862 bonds, 36 pseudobonds, 9991 residues, 3 models selected  

> select clear

Drag select of 341 residues, 1 pseudobonds  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #1/C #1/E #1/F #3/A

Alignment identifier is 1  

> select #1/E-F:12-690 #3/A:540-690

9510 atoms, 9644 bonds, 10 pseudobonds, 1404 residues, 4 models selected  

> ui tool show Matchmaker

> matchmaker #1/E & sel to #2/A pairing ss

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 169, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 288, in run_matchmaker  
run(self.session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 730, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
KeyError: <chimerax.atomic.molobject.StructureSeq object at 0x7cab68e48700>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: REMBRANDT (rembrandt, LLVM 15.0.7, DRM 3.54, 6.5.0-26-generic)
OpenGL vendor: AMD

Python: 3.9.11
Locale: it_IT.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 82SC
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 7 6800H with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            14Gi       6.6Gi       5.1Gi        85Mi       3.1Gi       7.8Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA107M [GeForce RTX 3050 Ti Mobile] [10de:25a0] (rev a1)	
	Subsystem: Lenovo GA107M [GeForce RTX 3050 Ti Mobile] [17aa:3af8]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0