AlphaFold coloring panel does not list AlphaFold models in menu

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.6-x86_64-i386-64bit
ChimeraX Version: 1.6.dev202211082330 (2022-11-08 23:30:49 UTC)
Description
AlphaFold coloring gui does not show Alphafold database model opened from a file in the menu of Residues to color because it doesn't realize it is an AlphaFold model.  It does not have a "alphafold" attribute and does not have AlphaFold in its name.

Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.6.dev202211082330 (2022-11-08)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/Downloads/ChimeraX/AlphaFold/AF-D5EHC5-F1-model_v4.cif
> format mmcif

Chain information for AF-D5EHC5-F1-model_v4.cif #1  
---  
Chain | Description | UniProt  
A | Aminotransferase class IV | D5EHC5_AMICL  
  

> ui tool show AlphaFold




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
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      Time since boot: 62 days 21:37

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[Tom Goddard]

The mmCIF AlphaFold database models have a "_database_2" table that ChimeraX reads with a database id "AlphaFoldDB". But predicted PDB structure file have no REMARK records at all and nothing that would indicate they are from AlphaFold in the file. Seems erratic to try to guess from the file name. It may be better to allow all models in the menu. The coloring choices use bfactor ("confidence") and some attributes assigned by aligning to an experimental structure (CA distance, missing structure, different sequence). The alignment attributes won't be present in a newly opened structure that was not aligned. And non-alphafold models with not have confidence (ie plddt) in the bfactor column. But we can leave it up to the user to decide if the model is an alphafold model.

[Tom Goddard]

Fixed.

Show all structures in alphafold coloring gui but set the menu entry initially to first identified as an AlphaFold model using name, alphafold attribute, or mmcif database_2 entry.