AlphaFold: 'AtomicStructure' object has no attribute 'num_observed_residues'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7.dev202306162113 (2023-06-16 21:13:38 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7.dev202306162113 (2023-06-16)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\User\Documents\Phd Project related\Alphafold2
> results\TbiB1_PAPAP_HpNGTvsANVTK_87cd3.result\TbiB1_PAPAP_HpNGTvsANVTK_87cd3\TbiB1_PAPAP_HpNGTvsANVTK_87cd3_unrelaxed_rank_002_alphafold2_multimer_v3_model_5_seed_000.pdb"
> format pdb

Chain information for
TbiB1_PAPAP_HpNGTvsANVTK_87cd3_unrelaxed_rank_002_alphafold2_multimer_v3_model_5_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show AlphaFold

> alphafold predict #1/A

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
[Repeated 1 time(s)]

> color /B sky blue

Running AlphaFold prediction  
[Repeated 1 time(s)]AlphaFold prediction finished  
Results in C:\Users\User/Downloads/ChimeraX/AlphaFold/prediction_1  

> open C:\Users\User/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb

Alphafold structure best_model.pdb has 2 chains (A, B), expected 1. Not
renaming chain id to match target structure.  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\predict.py", line 231, in _unzip_results  
self._open_prediction()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\predict.py", line 212, in _open_prediction  
self.session.models.add(models)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\models.py", line 728, in add  
m.added_to_session(session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\fetch.py", line 100, in _show_chain_table  
_log_chain_table([m], align_to_name, prediction_method=prediction_method)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 476, in _log_chain_table  
rows.append((cid,) + ids + (rmsd, m.num_residues, m.num_observed_residues,
pct_id))  
^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'AtomicStructure' object has no attribute
'num_observed_residues'  
  
AttributeError: 'AtomicStructure' object has no attribute
'num_observed_residues'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 476, in _log_chain_table  
rows.append((cid,) + ids + (rmsd, m.num_residues, m.num_observed_residues,
pct_id))  
^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
AlphaFold prediction finished  
Results in C:\Users\User/Downloads/ChimeraX/AlphaFold/prediction_1  

> open C:\Users\User/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb

Alphafold structure best_model.pdb has 2 chains (A, B), expected 1. Not
renaming chain id to match target structure.  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\predict.py", line 231, in _unzip_results  
self._open_prediction()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\predict.py", line 212, in _open_prediction  
self.session.models.add(models)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\models.py", line 728, in add  
m.added_to_session(session)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\fetch.py", line 100, in _show_chain_table  
_log_chain_table([m], align_to_name, prediction_method=prediction_method)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 476, in _log_chain_table  
rows.append((cid,) + ids + (rmsd, m.num_residues, m.num_observed_residues,
pct_id))  
^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'AtomicStructure' object has no attribute
'num_observed_residues'  
  
AttributeError: 'AtomicStructure' object has no attribute
'num_observed_residues'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 476, in _log_chain_table  
rows.append((cid,) + ids + (rmsd, m.num_residues, m.num_observed_residues,
pct_id))  
^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4887
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: HP
Model: HP EliteBook 840 G8 Notebook PC
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 16,844,550,144
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1145G7 @ 2.60GHz
OSLanguage: en-US

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[Tom Goddard]

The user ran an AlphaFold prediction of a single chain #1/A, but the prediction model had 2 chains. ChimeraX warned about that but then logging failed because of the unusual code path. While I could protect against this, it is so weird and rare I don't think I should try to handle AlphaFold returning such unexpected results.

My best guess as to how this happened is that the user started the AlphaFold run, but pressed Cancel in the "Allow non-Google code to run", then inserted a comma in the sequence, possibly accidentally or maybe on purpose, and then ran the prediction.