ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.7.3-arm64-arm-64bit
ChimeraX Version: 1.12rc202605142114 (2026-05-14 21:14:16 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.12rc202605142114 (2026-05-14)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1XEO format mmcif fromDatabase pdbe_bio

Summary of feedback from opening 1XEO fetched from pdbe_bio  
---  
warning | Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
1XEO bioassembly 1 title:  
High Resolution Crystals Structure of Cobalt- Peptide Deformylase Bound To
Formate [more info...]  
  
Chain information for 1XEO bioassembly 1 #1  
---  
Chain | Description  
A | Peptide deformylase  
  
Non-standard residues in 1XEO bioassembly 1 #1  
---  
CO — (CO)  
FMT — (FMT)  
  
2 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  
Opened 1 biological assemblies for 1XEO  

> open /Users/allisonjudge/Desktop/Gammanonin/MVA_no-peptide.pdb

> combine #1 #2

Remapping chain ID 'A' in MVA_no-peptide.pdb #2 to 'E'  
Computing secondary structure  
[Repeated 1 time(s)]

> hide #1 models

> hide #2 models

> select #3/A:129

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

> show sel atoms

> select #3/A:129@SG

1 atom, 1 residue, 1 model selected  

> select add #3@@serial_number=1561

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> bond length #3/A:129@SG#3/E:1@C 2

> select #3@@serial_number=1563

1 atom, 1 residue, 1 model selected  

> select add #3@@serial_number=1578

2 atoms, 2 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Minimize Structure"

Populating font family aliases took 189 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.  

> minimize #3

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Filling out missing side chains  
combination #3/A LYS 165: phi 65.8, psi none trans  
Applying LYS rotamer (chi angles: -165.2 -87.2 -177.2 -178.9) to combination
#3/A LYS 165  
Summary of feedback from adding hydrogens to combination #3  
---  
warnings | Not adding hydrogens to combination #3/E VAL 1 N because it is missing heavy-atom bond partners  
Not adding hydrogens to combination #3/E VAL 1 CA because it is missing heavy-
atom bond partners  
Not adding hydrogens to combination #3/E VAL 1 H because it is missing heavy-
atom bond partners  
Not adding hydrogens to combination #3/E VAL 1 HA because it is missing heavy-
atom bond partners  
Not adding hydrogens to combination #3/E VAL 1 HB because it is missing heavy-
atom bond partners  
6 messages similar to the above omitted  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: combination #3/E VAL 1 N  
notes | No usable SEQRES records for combination (#3) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: combination #3/A SER 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: combination #3/A LYS 165  
159 hydrogen bonds  
combination #3/A LYS 165 is not terminus, removing H atom from 'C'  
1374 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen combination #3/E VAL 1 H bonded to atom in diffent residue
(combination #3/E VAL 1 N)  

> select #3@@serial_number=1566

1 atom, 1 residue, 1 model selected  

> select add #3@@serial_number=1568

2 atoms, 1 residue, 1 model selected  

> select add #3@@serial_number=1567

3 atoms, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3@@serial_number=1570

1 atom, 1 residue, 1 model selected  

> select add #3/A:129@HB3

2 atoms, 2 residues, 1 model selected  

> select subtract #3/A:129@HB3

1 atom, 1 residue, 1 model selected  

> select add #3@@serial_number=1575

2 atoms, 1 residue, 1 model selected  

> select add #3@@serial_number=1577

3 atoms, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3@@serial_number=1576

1 atom, 1 residue, 1 model selected  

> select add #3@@serial_number=1572

2 atoms, 1 residue, 1 model selected  

> select add #3@@serial_number=1574

3 atoms, 1 residue, 1 model selected  

> select add #3@@serial_number=1573

4 atoms, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3@@serial_number=1571

1 atom, 1 residue, 1 model selected  

> select add #3@@serial_number=1564

2 atoms, 2 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3/A:129@HB3

1 atom, 1 residue, 1 model selected  

> select add #3/A:129@HB2

2 atoms, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Minimize Structure"

> minimize #3

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Filling out missing side chains  
combination #3/A LYS 165: phi 65.8, psi none trans  
Applying LYS rotamer (chi angles: -160.1 -90.5 -80.9 68.3) to combination #3/A
LYS 165  
Summary of feedback from adding hydrogens to combination #3  
---  
warnings | Not adding hydrogens to combination #3/E VAL 1 N because it is missing heavy-atom bond partners  
Not adding hydrogens to combination #3/E VAL 1 CA because it is missing heavy-
atom bond partners  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: combination #3/E VAL 1 N  
notes | No usable SEQRES records for combination (#3) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: combination #3/A SER 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: combination #3/A LYS 165  
152 hydrogen bonds  
combination #3/A LYS 165 is not terminus, removing H atom from 'C'  
23 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue FMT (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/yl/8263z7355g9fy0j9clyyq3p00000gn/T/tmpw4n9f8z6/ante.in.mol2 -fi
mol2 -o
/var/folders/yl/8263z7355g9fy0j9clyyq3p00000gn/T/tmpw4n9f8z6/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(FMT) ``  
(FMT) `Welcome to antechamber 20.0: molecular input file processor.`  
(FMT) ``  
(FMT) `Info: Finished reading file
(/var/folders/yl/8263z7355g9fy0j9clyyq3p00000gn/T/tmpw4n9f8z6/ante.in.mol2);
atoms read (7), bonds read (6).`  
(FMT) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(FMT) `Running:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(FMT) ``  
(FMT) ``  
(FMT) `Running:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(FMT) `Info: Total number of electrons: 26; net charge: 0`  
(FMT) ``  
(FMT) `Running:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(FMT) ``  
(FMT) `Running:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(FMT) ``  
(FMT) `Running:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(FMT) ``  
Charges for residue FMT determined  
Assigning partial charges to residue UNK (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/yl/8263z7355g9fy0j9clyyq3p00000gn/T/tmpzjpx709f/ante.in.mol2 -fi
mol2 -o
/var/folders/yl/8263z7355g9fy0j9clyyq3p00000gn/T/tmpzjpx709f/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(UNK) ``  
(UNK) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNK) ``  
(UNK) `Info: Finished reading file
(/var/folders/yl/8263z7355g9fy0j9clyyq3p00000gn/T/tmpzjpx709f/ante.in.mol2);
atoms read (16), bonds read (15).`  
(UNK) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNK) `Running:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNK) ``  
(UNK) ``  
(UNK) `Running:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNK) `Info: Total number of electrons: 56; net charge: -2`  
(UNK) ``  
(UNK) `Running:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNK) ``  
(UNK) `Running:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(UNK) ``  
(UNK) `Running:
/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNK) ``  
Charges for residue UNK determined  

1 structure has non-integral total charge.  
Details in log.  

Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:  
combination #3: combination #3/E VAL 1: -0.4157 and combination #3/E VAL 1:
0.0469  
Dock prep finished  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 116, in minimize  
run(self.session, cmd)  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 132, in prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 156, in run_steps  
callback()  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 131, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 45, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 231, in _minimize  
forcefield.registerResidueTemplate(template)  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 476, in registerResidueTemplate  
raise ValueError('Residue template %s with the same override level %d already
exists.' % (template.name, template.overrideLevel))  
ValueError: Residue template E-VAL-1 with the same override level 0 already
exists.  
  
ValueError: Residue template E-VAL-1 with the same override level 0 already
exists.  
  
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 476, in registerResidueTemplate  
raise ValueError('Residue template %s with the same override level %d already
exists.' % (template.name, template.overrideLevel))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac16,12
      Model Number: MW103LL/A
      Chip: Apple M4
      Total Number of Cores: 10 (4 performance and 6 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.3 (24G419)
      Kernel Version: Darwin 24.6.0
      Time since boot: 44 days, 3 hours, 52 minutes

Graphics/Displays:

    Apple M4:

      Chipset Model: Apple M4
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.2.0
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    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: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    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: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12rc202605142114
    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: 1.2.1
    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: 1.4.1
    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: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.1
    ChimeraX-MatchMaker: 2.4
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.8
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    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: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    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: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.6
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    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: 8.4.0
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.15
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    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: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.21.2
    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
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.9.6
    plotly: 6.7.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.17.1
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    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: 6.10.2
    PyQt6-Qt6: 6.10.1
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.1
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.29
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 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: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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: 3.4.4
    stack-data: 0.6.3
    starlette: 1.0.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.5
    tqdm: 4.67.3
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    Unidecode: 1.4.0
    urllib3: 2.7.0
    uvicorn: 0.47.0
    wcwidth: 0.7.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.23.0