AlphaFold Error Plot gui may fetch PAE with the wrong database version

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.4-arm64-arm-64bit
ChimeraX Version: 1.5.dev202207201858 (2022-07-20 18:58:08 UTC)
Description
If and AlphaFold database structure is fetched using a specific version of the database (e.g. with alphafold fetch command with version option), and then later the PAE data is fetched using the AlphaFold Error Plot GUI, then it can easily get the wrong PAE file corresponding to a different version of the database.

A few things could help mitgate this problem.  First if the directory with the structure contains the PAE data already, then use that file.  Currently the GUI instead offers to get the file based on uniprot id.  If the PAE has not already been fetched, when the GUI fetches it can look at the structure name and if it ends in a version number e.g. "_v3" and that version is different then the default pae fetch then use the file suffix version and warn that this was done.

Log:
UCSF ChimeraX version: 1.5.dev202207201858 (2022-07-20)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/goddard/Downloads/ChimeraX/AlphaFold/AF-A0A4T0DZS4-F1-model_v3.cif
> format mmcif

Chain information for AF-A0A4T0DZS4-F1-model_v3.cif #1  
---  
Chain | Description | UniProt  
A | M-phase inducer phosphatase | A0A4T0DZS4_AURPU  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/goddard/Downloads/ChimeraX/AlphaFold/AF-A0A4T0DZS4-F1-predicted_aligned_error_v3.json

> alphafold pae #1 uniprotId A0A4T0DZS4

Fetching url
https://alphafold.ebi.ac.uk/files/AF-A0A4T0DZS4-F1-predicted_aligned_error_v2.json
failed: HTTP Error 404: Not Found  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 7459.121.3
      OS Loader Version: 7459.121.3

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 64 days 12:22

Graphics/Displays:

    Apple M1 Max:

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      Type: GPU
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      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
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[Tom Goddard]

Inspecting the AlphaFold Database version 3 mmCIF file AF-A0A4T0DZS4-F1-model_v3.cif I did not see any table in the file that indicates this is a version 3 files. So it does not appear that we can tell the version from the metadata in the file and will have to rely on the file name suffix ("_v3"). Probably should ask EBI to in the future add the version of the database in the metadata.

[Tom Goddard]

Fixed.

I made the AlphaFold Error Plot tool look at the structure file path and if it appears to be of the form of database file names with the version number then use that version number from the file name and log a warning if that is not the default version number. For example AF-A0A4T0DZS4-F1-model_v3.cif would use version 3. The filename match looks for starting "AF", ending in ".cif" or ".pdb" and having "_v#" at the end of the name.