ProNA3D TypeError: Logger.error() got an unexpected keyword argument 'log'

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-26.4.1-arm64-arm-64bit
ChimeraX Version: 1.13.dev202605052233 (2026-05-05 22:33:02 UTC)
Description
Tried ProNA3D with AlphaFold 3 model and all ProNA3D advanced settings for AlphaFold enabled and got this error.

Log:
UCSF ChimeraX version: 1.13.dev202605052233 (2026-05-05)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed install /Users/goddard/Downloads/ChimeraX_ProNA3D-0.1-py3-none-
> any.whl

Installed ChimeraX-ProNA3D (0.1)  

> ui tool show ProNA3D

Please register the custom scheme 'prona3d' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

> open 9urm

Summary of feedback from opening 9urm fetched from pdb  
---  
note | Fetching compressed mmCIF 9urm from http://files.rcsb.org/download/9urm.cif  
  
9urm title:  
HRV14 3C in complex with single chain antibody YDF and cloverleafRNA-
conformation1 splitRNA [more info...]  
  
Chain information for 9urm #1  
---  
Chain | Description | UniProt  
A | Protease 3C | POLG_HRV14 2-181  
B | YDF H chain |   
C | YDF L chain |   
R | RNA (83-MER) |   
  

> select /A:2-180

1382 atoms, 1403 bonds, 179 residues, 1 model selected  

### ProNA3D Cluster Analysis Results

  

Cluster information for 9urm [A, R]  
---  
Cluster| Residues  
1| A:82, R:49, A:80, R:71, R:72, A:84, R:50, R:48, A:81, A:83, A:85, R:47  
2| A:6, R:61, A:153, R:60, A:13, R:63, A:155, A:154, A:5, R:62, A:89, A:9,
A:12  
  
  
  
Calculation of interface was successful  
Interface plot saved to: /Users/goddard/Desktop/interface_plot.png  

> log metadata #1

Metadata for 9urm #1  
---  
Title | HRV14 3C in complex with single chain antibody YDF and cloverleafRNA-conformation1 splitRNA  
Citation | Yang, B., Wang, Q., Sun, S.W., Zhang, X. (?). HRV14 3C in complex with single chain antibody YDF and cloverleafRNA-conformation1 splitRNA. To Be Published  
Gene sources | rhinovirus B14  
Homo sapiens  
CryoEM Map | EMDB 64461 — open map  
Experimental method | Electron microscopy  
Resolution | 4.24Å  
  
> open 64461 fromDatabase emdb

Summary of feedback from opening 64461 fetched from emdb  
---  
notes | Fetching compressed map 64461 from https://files.wwpdb.org/pub/emdb/structures/EMD-64461/map/emd_64461.map.gz  
Fetching map header 64461 from
https://files.wwpdb.org/pub/emdb/structures/EMD-64461/header/emd-64461.xml  
  
Opened emdb 64461 as #2, grid size 280,280,280, pixel 0.96, shown at level
0.06, step 1, values float32, fit PDB 9urm  
Chain1 is equal to chain2!  

### ProNA3D Cluster Analysis Results

  

Cluster information for 9urm [A, R]  
---  
Cluster| Residues| Zone  
1| A:82, R:49, A:80, R:71, R:72, A:84, R:50, R:48, A:81, A:83, A:85, R:47|
Zone in Cluster Nr 1  
2| A:6, R:61, A:153, R:60, A:13, R:63, A:155, A:154, A:5, R:62, A:89, A:9,
A:12| Zone in Cluster Nr 2  
  
  
  
Calculation of interface was successful  

> volume zone #2 nearAtoms #1/A:82 #1/R:49 #1/A:80 #1/R:71 #1/R:72 #1/A:84
> #1/R:50 #1/R:48 #1/A:81 #1/A:83 #1/A:85 #1/R:47 range 5

> volume zone #2 nearAtoms #1/A:6 #1/R:61 #1/A:153 #1/R:60 #1/A:13 #1/R:63
> #1/A:155 #1/A:154 #1/A:5 #1/R:62 #1/A:89 #1/A:9 #1/A:12 range 5

> close

> open 9obd

Summary of feedback from opening 9obd fetched from pdb  
---  
notes | Fetching compressed mmCIF 9obd from http://files.rcsb.org/download/9obd.cif  
Fetching CCD A1CAK from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/A1CAK/A1CAK.cif  
Fetching CCD A1CAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/A1CAL/A1CAL.cif  
Fetching CCD F2T from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/F2T/F2T.cif  
Fetching CCD RFJ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/J/RFJ/RFJ.cif  
  
9obd title:  
Crystal structure of human Argonaute2 in complex with a fully modified siRNA
with a 5'-phenylpropargyl phosphate [more info...]  
  
Chain information for 9obd #1  
---  
Chain | Description | UniProt  
A | Protein argonaute-2 | AGO2_HUMAN 1-859  
B | fully modified siRNA with a 5' phenylpropargyl phosphate |   
  
Non-standard residues in 9obd #1  
---  
IPA — isopropyl alcohol (2-propanol)  
IPH — phenol  
MG — magnesium ion  
  

> ui tool show OpenFold

> openfold predict protein /A rna /B ligandCcd MG,IPH(3),IPA(2) name 9obd

Running OpenFold prediction of protein with 859 residues, nucleic acid
sequence with 21 residues, 6 ligands IPA (2), IPH (3), MG on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence pTM 0.93, ipTM 0.84, pLDDT 84  
OpenFold prediction completed in 573 seconds (start openfold 13 sec,
initialize neural net 29 sec, sequence search 109 sec, structure inference 387
sec)  
Please cite OpenFold-1 Democratizing Biomolecular Interaction Modeling.
BioRxiv https://doi.org/10.1101/2024.11.19.624167 if you use these
predictions.  

> open
> /Users/goddard/Desktop/openfold/9obd/9obd/seed_42/9obd_seed_42_sample_1_model.cif
> logInfo false

Matchmaker 9obd, chain A (#1) with 9obd_seed_42_sample_1_model.cif, chain A
(#2), sequence alignment score = 4383.3  
RMSD between 698 pruned atom pairs is 0.780 angstroms; (across all 810 pairs:
1.574)  
  

> open /Users/goddard/ucsf/data/alphafold3/fold_9obd/fold_9obd_model_0.cif

Chain information for fold_9obd_model_0.cif #3  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> mmaker #3 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 9obd, chain A (#1) with fold_9obd_model_0.cif, chain A (#3),
sequence alignment score = 4371.3  
RMSD between 691 pruned atom pairs is 0.586 angstroms; (across all 810 pairs:
1.713)  
  

> ui tool show ProNA3D

Please register the custom scheme 'prona3d' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

> hide #2 models

> hide #!1 models

### ProNA3D Cluster Analysis Results

  

Cluster information for fold_9obd_model_0.cif [A, B]  
---  
Cluster| Residues  
1| A:545, B:1, A:524, A:670, B:11, A:339, B:21, A:635, B:10, A:551, B:2,
A:548, A:68, B:14, A:179, B:13, A:280, B:17, A:761, B:8, A:757, B:6, A:529,
B:15, A:337, B:20, A:67, B:16, A:792, B:3, A:312, A:277, A:222, A:790, B:4,
A:126, A:600, A:756, B:5, A:570, A:335, B:19, A:351, B:9, A:559, A:804, A:566,
A:178, A:526, A:547, A:672, A:97, A:66, A:710, A:128, B:7, A:674, B:12, A:759,
A:65, A:603, A:562, B:18, A:797, A:675, A:546, A:525, A:311, A:760, A:294,
A:331, A:296, A:602, A:753, A:798, A:368, A:221, A:336, A:637, A:316, A:795,
A:601, A:793, A:332, A:353, A:365, A:563, A:815, A:361, A:70, A:72, A:220,
A:859, A:295, A:758, A:177, A:338, A:122, A:754, A:533, A:544, A:364, A:714,
A:709, A:375, A:279, A:176, A:63, A:266, A:278, A:812, A:275, A:308, A:69,
A:522, A:814, A:755, A:799, A:558, A:671, A:369, A:811, A:796, A:271, A:272  
  
  
  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 316, in interceptRequest  
self._callback(info)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 543, in thread_safe  
func(*args, **kw)  
File "/Users/goddard/Library/Application
Support/ChimeraX/1.13/lib/python/site-packages/chimerax/ProNA3D/tool.py", line
474, in handle_scheme  
self.session.logger.error('Mean pLDDT calculation requires "AlphaFold
Prediction" to be selected as Input Type.', log=True)  
TypeError: Logger.error() got an unexpected keyword argument 'log'  
  
TypeError: Logger.error() got an unexpected keyword argument 'log'  
  
File "/Users/goddard/Library/Application
Support/ChimeraX/1.13/lib/python/site-packages/chimerax/ProNA3D/tool.py", line
474, in handle_scheme  
self.session.logger.error('Mean pLDDT calculation requires "AlphaFold
Prediction" to be selected as Input Type.', log=True)  
  
See log for complete Python traceback.  
  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
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: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 Performance and 8 Efficiency)
      Memory: 64 GB
      System Firmware Version: 18000.101.7
      OS Loader Version: 18000.101.7

Software:

    System Software Overview:

      System Version: macOS 26.4.1 (25E253)
      Kernel Version: Darwin 25.4.0
      Time since boot: 9 days, 48 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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: 4.1.2
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.8.3
    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: 1.13.dev202605052233
    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
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    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
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    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
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    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
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    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
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    ChimeraX-ProNA3D: 0.1
    ChimeraX-PubChem: 2.2
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    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
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    ChimeraX-RenumberResidues: 1.1
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    ChimeraX-RNALayout: 1.0
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    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
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    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
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    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
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    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
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    ChimeraX-TapeMeasure: 1.0
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    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
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    ChimeraX-VIPERdb: 1.0
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    ChimeraX-WavefrontOBJ: 1.0
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    psutil: 7.0.0
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    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
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File attachment: fold_9obd.zip

fold_9obd.zip​

[goddard@…]

Added by email2trac

[Tom Goddard]

ProNA3D was trying to give me an error message that I had to select AlphaFold Prediction as the input type, but the error reporting call had a bad function argument "log = True" that only applies to logger status messages.