Error in atom spec evaluation

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Tried to make electrostatic surface of the protein

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/80S_HERC5-dimer1-517-coot-4.pdb

Summary of feedback from opening
D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/80S_HERC5-dimer1-517-coot-4.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU D 5 PHE D 9 1 5  
Start residue of secondary structure not found: HELIX 2 2 PHE D 17 PHE D 21 1
5  
Start residue of secondary structure not found: HELIX 3 3 ASP D 26 LYS D 37 1
12  
Start residue of secondary structure not found: HELIX 4 4 ASN I 51 ARG I 63 1
13  
Start residue of secondary structure not found: HELIX 5 5 ASP A 33 GLY A 39 1
7  
195 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 201 201 GLY b 105 LEU b
118 1 14  
Start residue of secondary structure not found: HELIX 202 202 SER c 10 MET c
22 1 13  
Start residue of secondary structure not found: HELIX 203 203 GLY c 30 GLN c
40 1 11  
Start residue of secondary structure not found: HELIX 204 204 PRO c 53 LYS c
68 1 16  
Start residue of secondary structure not found: HELIX 205 205 ASN c 77 CYS c
85 1 9  
Start residue of secondary structure not found: HELIX 206 206 ILE d 29 HIS d
34 1 6  
648 messages similar to the above omitted  
Cannot find LINK/SSBOND residue K (5360 )  
Cannot find LINK/SSBOND residue A (2529 )  
Cannot find LINK/SSBOND residue G (2584 )  
Cannot find LINK/SSBOND residue G (2331 )  
Cannot find LINK/SSBOND residue C (2411 )  
1015 messages similar to the above omitted  
  
Chain information for 80S_HERC5-dimer1-517-coot-4.pdb #1  
---  
Chain | Description  
8 | No description available  
CD | No description available  
CI | No description available  
L5 | No description available  
L7 | No description available  
L8 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LR | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LW | No description available  
LX | No description available  
LY | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Ld | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Lh | No description available  
Li | No description available  
Lj | No description available  
Lk | No description available  
Ll | No description available  
Lm | No description available  
Ln | No description available  
Lo | No description available  
Lp | No description available  
Lr | No description available  
Ls | No description available  
Lt | No description available  
Pt | No description available  
S2 | No description available  
SA | No description available  
SB | No description available  
SC | No description available  
SD | No description available  
SE | No description available  
SF | No description available  
SG | No description available  
SH | No description available  
SI | No description available  
SJ | No description available  
SK | No description available  
SL | No description available  
SM | No description available  
SN | No description available  
SO | No description available  
SP | No description available  
SQ | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SU | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SY | No description available  
SZ | No description available  
Sa | No description available  
Sb | No description available  
Sc | No description available  
Sd | No description available  
Se | No description available  
Sf | No description available  
Sg | No description available  
a b | No description available  
  
23 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> show cartoons

Computing secondary structure  

> hide atoms

> select /a

8006 atoms, 8189 bonds, 999 residues, 1 model selected  

> save D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono1.pdb selectedOnly
> true

> select /b

8004 atoms, 8188 bonds, 997 residues, 1 model selected  

> save D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono2.pdb selectedOnly
> true relModel #1

> open D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono1.pdb
> D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono2.pdb

Summary of feedback from opening
D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLNCD 6 GLYCD 8 1 3  
Start residue of secondary structure not found: HELIX 2 2 ASPCD 18 LEUCD 20 1
3  
Start residue of secondary structure not found: HELIX 3 3 PROCD 27 ASNCD 36 1
10  
Start residue of secondary structure not found: HELIX 4 4 GLNCI 52 VALCI 62 1
11  
Start residue of secondary structure not found: HELIX 5 5 PHELA 34 HISLA 38 1
5  
901 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYSS (121 )  
Cannot find LINK/SSBOND residue CYSS (121 )  
Cannot find LINK/SSBOND residue CYSS (121 )  
Cannot find LINK/SSBOND residue CYSS (126 )  
Cannot find LINK/SSBOND residue CYSS (126 )  
2 messages similar to the above omitted  
  
Summary of feedback from opening
D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLNCD 6 GLYCD 8 1 3  
Start residue of secondary structure not found: HELIX 2 2 ASPCD 18 LEUCD 20 1
3  
Start residue of secondary structure not found: HELIX 3 3 PROCD 27 ASNCD 36 1
10  
Start residue of secondary structure not found: HELIX 4 4 GLNCI 52 VALCI 62 1
11  
Start residue of secondary structure not found: HELIX 5 5 PHELA 34 HISLA 38 1
5  
897 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYSS (121 )  
Cannot find LINK/SSBOND residue CYSS (121 )  
Cannot find LINK/SSBOND residue CYSS (121 )  
Cannot find LINK/SSBOND residue CYSS (126 )  
Cannot find LINK/SSBOND residue CYSS (126 )  
2 messages similar to the above omitted  
  
Chain information for mono1.pdb #2  
---  
Chain | Description  
a | No description available  
  
Chain information for mono2.pdb #3  
---  
Chain | Description  
b | No description available  
  

> hide #!1 models

> select #2/a:774

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #2

8006 atoms, 8189 bonds, 999 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen copy of mono1.pdb #/a ALA 365 H bonded to atom that should not have
hydrogens (copy of mono1.pdb #/a ALA 365 C)  

> select H

Nothing selected  

> select 365

Expected an objects specifier or a keyword  

> select :365

75 atoms, 70 bonds, 9 residues, 3 models selected  

> close #1

> select :365

10 atoms, 8 bonds, 2 residues, 2 models selected  

> delete sel

> select add #2

8001 atoms, 8184 bonds, 998 residues, 1 model selected  

> coulombic sel

Traceback (most recent call last):  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\std_commands\defattr.py", line 185, in defattr  
objects = atom_spec.evaluate(session, models=restriction)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 1157, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 1067, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 1070, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 511, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 673, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 693, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 628, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 617, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 635, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1024, in atomspec_filter  
return self._atomspec_filter_residue(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1089, in _atomspec_filter_residue  
selected = self._atomspec_attr_filter(atoms.residues, selected, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1061, in _atomspec_attr_filter  
selected = [(selected[i] and choose(obj)) for i, obj in enumerate(objects)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1061, in <listcomp>  
selected = [(selected[i] and choose(obj)) for i, obj in enumerate(objects)]  
~~~~~~~~^^^  
IndexError: tuple index out of range  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1420, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1393, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 403, in try_shortcut  
self.run_shortcut(keys)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 421, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 340, in run  
f(s)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip  
func(cmd + " %s")(session)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 594, in run_expanded_command  
run(session, cmd)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 537, in run  
run_command(session, command, **kw)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 110, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 34, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 81, in add_standard_charges  
defattr(session, attr_file, restriction=structures, summary=False)  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\std_commands\defattr.py", line 187, in defattr  
raise SyntaxError("Error evaluating atom specifier (%s) on line %d of %s: %s"  
SyntaxError: Error evaluating atom specifier (::amber_name=ARG @oxt,ot2,2oct)
on line 179 of D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\add_charge\amber_name.defattr: tuple index out of range  
  
SyntaxError: Error evaluating atom specifier (::amber_name=ARG @oxt,ot2,2oct)
on line 179 of D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\add_charge\amber_name.defattr: tuple index out of range  
  
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\std_commands\defattr.py", line 187, in defattr  
raise SyntaxError("Error evaluating atom specifier (%s) on line %d of %s: %s"  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 591.74
OpenGL renderer: NVIDIA GeForce RTX 4080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z790 AORUS ELITE AX
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 137,254,060,032
MaxProcessMemory: 137,438,953,344
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900KF
OSLanguage: en-US

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2026.1.4
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0

[Eric Pettersen]

Would need a test code to tinker with this complicated code