alphafold match not finding model

[luki.bauer94@…]

The following bug report has been submitted:
Platform:        macOS-26.0-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Hi AlphaFold match does not work anymore with the Uniprot ID

alphafold match P02340
1 UniProt id does not have an AlphaFold database model: P02340 (UniProt P02340)

Sequence search found 1 AlphaFold id that do not have AlphaFold database models: P02340 (UniProt P02340)

No AlphaFold model with similar sequence for UniProt P02340

Opened 0 AlphaFold model

While there is clearly a AF DB model in Uniprot:
https://www.uniprot.org/uniprotkb/P02340/entry#structure

Thanks,

Lukas 


Log:
Startup Messages  
---  
note | CubeNTube: sphere eraser undo support enabled  
  
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold match P02340

1 UniProt id does not have an AlphaFold database model: P02340 (UniProt
P02340)  

Sequence search found 1 AlphaFold id that do not have AlphaFold database
models: P02340 (UniProt P02340)  

No AlphaFold model with similar sequence for UniProt P02340  

Opened 0 AlphaFold model  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M5
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: MacBook Pro
      Model Identifier: Mac17,2
      Model Number: MDE04D/A
      Chip: Apple M5
      Total Number of Cores: 10 (4 performance and 6 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 13822.1.2

Software:

    System Software Overview:

      System Version: macOS 26.0 (25A8353)
      Kernel Version: Darwin 25.0.0
      Time since boot: 7 Tage, 8 Stunden und 51 Minuten

Graphics/Displays:

    Apple M5:

      Chipset Model: Apple M5
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    aiohappyeyeballs: 2.6.1
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    build: 1.3.0
    certifi: 2025.7.14
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    cftime: 1.6.5
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[Eric Pettersen]

Reported by Lukas

[Tom Goddard]

The trouble is the AlphaFold database deleted the version 4 version of P02340, apparently when they updated to version 6.

The ChimeraX uses version 6 of the AlphaFold database by default and will fetch this file. In your current ChimeraX you can fetch it by specifying version 6.

open P02340 from alphafold version 6

Also ChimeraX checks for a new version of the alphafold database when you do a fetch if it has not checked in the last 24 hours. I've updated the server file that so it now says the current version is 6. So your ChimeraX should update to using version 6 automatically after 24 hours.