Alphafold contacts trying to create pseudobond involving deleted atoms

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/albihlw/Desktop/Test/fold_2024_06_07_15_23_model_0.cif

Chain information for fold_2024_06_07_15_23_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> alphafold contacts /A toResidues /B distance 3

Structure fold_2024_06_07_15_23_model_0.cif #1 does not have PAE data opened  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> C:/Users/albihlw/Desktop/Test/fold_2024_06_07_15_23_full_data_0.json

> alphafold contacts /A toResidues /B distance 3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\contacts.py", line 100, in alphafold_contacts  
b = g.new_pseudobond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.100.9955
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 5420
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 16,547,975,168
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
OSLanguage: en-US

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[Tom Goddard]

User tried alphafold contacts command from ChimeraX 1.7 on an AlphaFold 3 prediction and a C-alpha atom for a residue was not found. Probably the prediction involved nucleic acids, or possibly ligands. This should all work in current ChimeraX daily builds and 1.8.