ViewDock: hbonds not working

[iamkaant@…]

The following bug report has been submitted:
Platform:        macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.11.dev202508210112 (2025-08-21 01:12:24 UTC)
Description
Opened a protein pdb file and a multi-molecule mol2 file (DOCK output). In the ViewDock window clicked HBonds and clicked OK in the H-bond window.

Log:
UCSF ChimeraX version: 1.11.dev202508210112 (2025-08-21)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/LSD-WEBSITE/mPro/6y2g/rec.pdb format pdb

Chain information for rec.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> close session

> open
> /Users/ak87/ownCloud/owncloud/Calculations/NEOCORTEX/PROSPECTIVE/AMPC/rec.crg.pdb

Summary of feedback from opening
/Users/ak87/ownCloud/owncloud/Calculations/NEOCORTEX/PROSPECTIVE/AMPC/rec.crg.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
585 messages similar to the above omitted  
  
Chain information for rec.crg.pdb #1  
---  
Chain | Description  
B | No description available  
  
13 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> open /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/AmpC/ampc_xreal_mels_ifp_colored_abcdf.mol2

Opened ampc_xreal_mels_ifp_colored_abcdf.mol2 containing 1500 structures
(45878 atoms, 47580 bonds)  

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/AmpC/ampc_xreal_mels_chunk1.cxs

> hbonds #2.1-1500 restrict #1 & (main|ligand) reveal true

3227 hydrogen bonds found  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 429, in table_selection_changed  
self.update_model_description()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 497, in update_model_description  
if len(column_map[title].display_value(docking_structure)) > 20:  
~~~~~~~~~~^^^^^^^  
KeyError: 'hbonds'  
  
KeyError: 'hbonds'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 497, in update_model_description  
if len(column_map[title].display_value(docking_structure)) > 20:  
~~~~~~~~~~^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 227, in ok_cb  
results_callback(run(self.session,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 637, in process_hbonds  
self.update_model_description()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 497, in update_model_description  
if len(column_map[title].display_value(docking_structure)) > 20:  
~~~~~~~~~~^^^^^^^  
KeyError: 'hbonds'  
  
KeyError: 'hbonds'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/viewdock/tool.py", line 497, in update_model_description  
if len(column_map[title].display_value(docking_structure)) > 20:  
~~~~~~~~~~^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK193LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6 (24G84)
      Kernel Version: Darwin 24.6.0
      Time since boot: 16 днів і 3 хвилини

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
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    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.13
    ChimeraX-AtomicLibrary: 14.1.22
    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.dev202508210112
    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
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    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    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
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    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
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    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.5.1
    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: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
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    ChimeraX-PresetMgr: 1.1.3
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    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
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    ChimeraX-ResidueFit: 1.0.1
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    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.2.1
    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
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    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
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    ChimeraX-StructMeasure: 1.2.1
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    ChimeraX-Surface: 1.0.1
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    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
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    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.3
    ChimeraX-VIPERdb: 1.0
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    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
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    comm: 0.2.3
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[Eric Pettersen]

Hi Andrii: thanks for catching this! It will be fixed in the next build.

--Eric

Fix: ​https://github.com/RBVI/ChimeraX/commit/311544c2c26c162448658e772bf53c319dd6a447