Make AlphaFold database fetch handle isoforms

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Can't open AlphaFold database isoform structures.  When Foldseek returns such structures it produces an error.

Log:
UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open AF-Q8N9C0-2-F1-v6 format mmcif fromDatabase alphafold

UniProt identifiers must be 6 or 10 characters long, got "AF-Q8N9C0-2-F1-v6"  

> open AF-Q8N9C0-F1-v6 format mmcif fromDatabase alphafold

UniProt identifiers must be 6 or 10 characters long, got "AF-Q8N9C0-F1-v6"  

> open /Users/goddard/Downloads/AF-Q8N9C0-2-F1-model_v6.cif format mmcif

Chain information for AF-Q8N9C0-2-F1-model_v6.cif #1  
---  
Chain | Description | UniProt  
A | Immunoglobulin superfamily member 22 | IGS22_HUMAN 1-1326  
  
Color AF-Q8N9C0-2-F1-model_v6.cif by residue attribute pLDDT_score  

> ui tool show "Similar Structures"

> foldseek /A database afdb50

Error processing trigger "new frame":  
Foldseek results target header "AF-P11362-8-F1-model_v6 Fibroblast growth
factor receptor 1" did not have 3rd "-" separated field starting with "F"  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
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: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 13822.61.10

Software:

    System Software Overview:

      System Version: macOS 26.2 (25C56)
      Kernel Version: Darwin 25.2.0
      Time since boot: 26 days, 22 hours, 48 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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[Tom Goddard]

This problem was reported by David Miller on the ChimeraX mailing list.

​https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/QNTBBHPEYXWVYEMCOKHUF637XDEJF7DC/

[Tom Goddard]

Fixed.

I made foldseek on alphafold database correctly handle search results that contain isoform predictions. Also I made fetching from the AlphaFold database accept IDs of the following forms P29474, IGS22_HUMAN, Q8N9C0-2, AF-Q8N9C0-F1-v6, AF-Q8N9C0-2-F1-v6. Formerly it only accepted uniprot ids and uniprot names (1st and 2nd examples). Now the isoform number can be included after a dash. The first isoform does not have "-1" in the AlphaFold convention and Q8N9C0-1 won't work, you have to use Q8N9C0. The versions that start with AF are full AlphaFold database ids that include the Uniprot id, optional isoform number, fragment number (F1), and AF database version (v6). The fragment number is for large structures (I think larger than 1200 amino acids) which the AFDB predicted in multiple overlapping chunks.