ViewDock opening a swissdock file: not enough values to unpack (expected 2, got 1)

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-26.5.1-arm64-arm-64bit
ChimeraX Version: 1.13.dev202606060209 (2026-06-06 02:09:47 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.13.dev202606060209 (2026-06-06)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ryanhartwell/Desktop/30AA_RH2b.pdb format pdb

Chain information for 30AA_RH2b.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select /A:1-30

371 atoms, 382 bonds, 30 residues, 1 model selected  

> ui tool show OpenFold

No molecules specified for OpenFold prediction  

> openfold predict protein /A name 30AA_Rhd

Running OpenFold prediction of protein with 30 residues on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Running openfold prediction failed with exit code 1:  
command:  
/Users/ryanhartwell/openfold3/bin/run_openfold predict
--query_json=30AA_Rhd.json --runner_yaml=msa_path.yaml
--num_diffusion_samples=1 --device=gpu  
stdout:  
Download openfold3-parameters/of3-p2-155k.pt from s3://openfold3-data to
/Users/ryanhartwell/.openfold3/of3-p2-155k.pt? (yes/no):  
stderr:  
W0722 15:10:57.189000 20148
torch/distributed/elastic/multiprocessing/redirects.py:35] NOTE: Redirects are
currently not supported in MacOs.  
2026-07-22 15:11:12,260 - INFO - Failed to extract font properties from
/System/Library/Fonts/Supplemental/NISC18030.ttf: Could not set the fontsize
(invalid pixel size; error code 0x17)  
2026-07-22 15:11:12,317 - INFO - Failed to extract font properties from
/System/Library/Fonts/LastResort.otf: tuple indices must be integers or
slices, not str  
2026-07-22 15:11:12,364 - INFO - Failed to extract font properties from
/System/Library/Fonts/Apple Color Emoji.ttc: Could not set the fontsize
(invalid pixel size; error code 0x17)  
2026-07-22 15:11:12,435 - INFO - Failed to extract font properties from
/System/Library/Fonts/SFIndia.ttc: Can not load face (SFNT font table missing;
error code 0x8e)  
2026-07-22 15:11:12,441 - INFO - generated new fontManager  
2026-07-22 15:11:37,521 - INFO - NumExpr defaulting to 10 threads.  
2026-07-22 15:11:40,761 - INFO - No inference_ckpt_path or inference_ckpt_name
provided, selecting default checkpoint.  
  
Aborted!  
  

Populating font family aliases took 40 ms. Replace uses of missing font family
"Calibri" with one that exists to avoid this cost.  

> openfold predict protein GCGPKGPKGPKGPOGPOGPOGDOGDOGDOC name 30AA_Rhd

Running OpenFold prediction of protein with 30 residues on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Running openfold prediction failed with exit code 1:  
command:  
/Users/ryanhartwell/openfold3/bin/run_openfold predict
--query_json=30AA_Rhd.json --runner_yaml=msa_path.yaml
--num_diffusion_samples=1 --device=gpu  
stdout:  
Download openfold3-parameters/of3-p2-155k.pt from s3://openfold3-data to
/Users/ryanhartwell/.openfold3/of3-p2-155k.pt? (yes/no):  
stderr:  
W0722 15:13:23.969000 20160
torch/distributed/elastic/multiprocessing/redirects.py:35] NOTE: Redirects are
currently not supported in MacOs.  
2026-07-22 15:13:26,131 - INFO - NumExpr defaulting to 10 threads.  
2026-07-22 15:13:26,482 - INFO - No inference_ckpt_path or inference_ckpt_name
provided, selecting default checkpoint.  
  
Aborted!  
  

> openfold predict protein GCGPKGPKGPKGPOGPOGPOGDOGDOGDOC name 30AA_Rhd

Running OpenFold prediction of protein with 30 residues on gpu  
Using cached multiple sequence alignment
/Users/ryanhartwell/Downloads/ChimeraX/OpenFoldMSA/30AA_Rhd_0  
Running openfold prediction failed with exit code 1:  
command:  
/Users/ryanhartwell/openfold3/bin/run_openfold predict
--query_json=30AA_Rhd.json --runner_yaml=msa_path.yaml --use_msa_server=false
--num_diffusion_samples=1 --device=gpu  
stdout:  
Download openfold3-parameters/of3-p2-155k.pt from s3://openfold3-data to
/Users/ryanhartwell/.openfold3/of3-p2-155k.pt? (yes/no):  
stderr:  
W0722 15:13:53.264000 20168
torch/distributed/elastic/multiprocessing/redirects.py:35] NOTE: Redirects are
currently not supported in MacOs.  
2026-07-22 15:13:54,916 - INFO - NumExpr defaulting to 10 threads.  
2026-07-22 15:13:55,151 - INFO - No inference_ckpt_path or inference_ckpt_name
provided, selecting default checkpoint.  
  
Aborted!  
  
OpenFold predicted structure is not open.  

> openfold predict protein /A name 30AA_Rhd

Running OpenFold prediction of protein with 30 residues on gpu  
Using cached multiple sequence alignment
/Users/ryanhartwell/Downloads/ChimeraX/OpenFoldMSA/30AA_Rhd  
Running openfold prediction failed with exit code 1:  
command:  
/Users/ryanhartwell/openfold3/bin/run_openfold predict
--query_json=30AA_Rhd.json --runner_yaml=msa_path.yaml --use_msa_server=false
--num_diffusion_samples=1 --device=gpu  
stdout:  
Download openfold3-parameters/of3-p2-155k.pt from s3://openfold3-data to
/Users/ryanhartwell/.openfold3/of3-p2-155k.pt? (yes/no):  
stderr:  
W0722 15:14:37.417000 20179
torch/distributed/elastic/multiprocessing/redirects.py:35] NOTE: Redirects are
currently not supported in MacOs.  
2026-07-22 15:14:39,662 - INFO - NumExpr defaulting to 10 threads.  
2026-07-22 15:14:40,021 - INFO - No inference_ckpt_path or inference_ckpt_name
provided, selecting default checkpoint.  
  
Aborted!  
  

> minimize sel maxSteps 200

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Summary of feedback from adding hydrogens to 30AA_RH2b.pdb #1  
---  
notes | Termini for 30AA_RH2b.pdb (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A GLY 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A CYS 30  
Chain-final residues that are not actual C termini:  
14 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HYP (net charge +1) with am1-bcc method  
HYP: number of electrons (100) + formal charge (+1) is odd; cannot compute
charges for radical species using AM1-BCC method  

> ui tool show ViewDock

> open /Users/ryanhartwell/Downloads/docktov2/files/receptor.pdb format
> swissdock

Summary of feedback from opening
/Users/ryanhartwell/Downloads/docktov2/files/receptor.pdb  
---  
warnings | Ignored bad PDB record found on line 7529  
  
  
Ignored bad PDB record found on line 7531  
  
Chain information for receptor.pdb #2  
---  
Chain | Description  
? | No description available  
A | No description available  
  
Computing secondary structure  

> ui mousemode right zoom

> hide #1 models

> ui mousemode right zoom

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,-63.416,0,1,0,69.122,0,0,1,9.953

> ui mousemode right zoom

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,-41.986,0,1,0,76.696,0,0,1,-6.27

> ui tool show ViewDock

> open /Users/ryanhartwell/Downloads/docktov2/files/ligand.pdb format
> swissdock

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 371, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 138, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 234, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 547, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 518, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/__init__.py", line 63, in open  
models, status = opener(session, data, file_name, True, True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/io.py", line 580, in open_swissdock  
k,v = line[7:].strip().split(': ')  
^^^  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/io.py", line 580, in open_swissdock  
k,v = line[7:].strip().split(': ')  
^^^  
  
See log for complete Python traceback.  
  

> ui tool show ViewDock

> open /Users/ryanhartwell/Downloads/docktov2/files/ligand.pdb format
> swissdock

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 371, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 138, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 234, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 547, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 518, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/__init__.py", line 63, in open  
models, status = opener(session, data, file_name, True, True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/io.py", line 580, in open_swissdock  
k,v = line[7:].strip().split(': ')  
^^^  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/io.py", line 580, in open_swissdock  
k,v = line[7:].strip().split(': ')  
^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M5
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: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac17,3
      Model Number: MDHE4LL/A
      Chip: Apple M5
      Total Number of Cores: 10 (4 Super and 6 Efficiency)
      Memory: 16 GB
      System Firmware Version: 18000.120.36
      OS Loader Version: 18000.120.36

Software:

    System Software Overview:

      System Version: macOS 26.5.1 (25F80)
      Kernel Version: Darwin 25.5.0
      Time since boot: 15 days, 20 hours, 36 minutes

Graphics/Displays:

    Apple M5:

      Chipset Model: Apple M5
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      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: No
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    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: 4.4.2
    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: 3.2.1
    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: 1.69.1
    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: 1.13.dev202606060209
    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-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.2
    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: 1.8.3
    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: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.4.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.17
    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-NMRSTAR: 1.0.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.16.2
    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: 1.9
    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: 2.19
    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: 1.20
    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: 1.51.3
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.3
    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: 8.4.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    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: 3.18
    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
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    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: 4.10.0
    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: 0.18.0
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    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: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    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: 0.0.32
    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: 2026.5.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    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: 1.2.1
    superqt: 0.7.6
    tables: 3.10.2
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.6
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.7.0
    uvicorn: 0.49.0
    wcwidth: 0.8.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.24.2

[Tom Goddard]

This ticket also shows OpenFold predictions all failing because the user does not have the OpenFold checkpoint file in ~/.openfold. They probably quit ChimeraX while it was installing OpenFold previously so the model parameters were not downloaded. Running a prediction then fails. I've made a separate ticket for this #20784.