No AlphaFold model for alpha fetch BLAST search

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Something wrong with the "alpha fetch" BLAST search, I think - it reports that it found a matching sequence (Q9H0A0), but there's no AFDB model, but if I actually do "alpha fetch Q9H0A0" it fetches it just fine.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> clipper init

> cofr centerOfView showPivot true

> camera ortho

> lighting simple

UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\Users\\\tcroll\\\Documents\\\Structures\\\NAT10\\\9j3c_dimer_CoA\\\9j3c_nat10_rebuilt.cif

Summary of feedback from opening
C:\\\Users\\\tcroll\\\Documents\\\Structures\\\NAT10\\\9j3c_dimer_CoA\\\9j3c_nat10_rebuilt.cif  
---  
warnings | Atom H5B1 is not in the residue template for COA /A:1001  
Atom H5B1 is not in the residue template for COA /B:1001  
  
Chain information for 9j3c_nat10_rebuilt.cif #1  
---  
Chain | Description  
A B | RNA cytidine acetyltransferase  
  

> clipper spotlight #1

Chain information for 9j3c_nat10_rebuilt.cif  
---  
Chain | Description  
1.2/A 1.2/B | RNA cytidine acetyltransferase  
  

> view /A:722

> select /A:723@CB

1 atom, 1 residue, 1 model selected  

> select add /A:724@CG

2 atoms, 2 residues, 1 model selected  

> alphafold match #1/A

Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  

Sequence search found 1 AlphaFold id that do not have AlphaFold database
models: Q9H0A0 (chain A)  

No AlphaFold model with similar sequence for chain A  

Opened 0 AlphaFold model  

> alphafold fetch Q9H0A0

Fetching compressed AlphaFold Q9H0A0 from
https://alphafold.ebi.ac.uk/files/AF-Q9H0A0-F1-model_v6.cif  
Chain information for AlphaFold Q9H0A0 #2  
---  
Chain | Description | UniProt  
A | RNA cytidine acetyltransferase | NAT10_HUMAN 1-1025  
  
Color AlphaFold Q9H0A0 by residue attribute pLDDT_score  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9j3c_nat10_rebuilt.cif, chain B (#1.2) with AlphaFold Q9H0A0, chain
A (#2), sequence alignment score = 4369.9  
RMSD between 629 pruned atom pairs is 1.004 angstroms; (across all 790 pairs:
1.699)  
  

> matchmaker #2 to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9j3c_nat10_rebuilt.cif, chain A (#1.2) with AlphaFold Q9H0A0, chain
A (#2), sequence alignment score = 4355.5  
RMSD between 640 pruned atom pairs is 0.996 angstroms; (across all 798 pairs:
1.757)  
  




OpenGL version: 3.3.0 NVIDIA 581.29
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

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[Tom Goddard]

Fixed in Oct 28 daily build.

The alphafold match command uses a k-mer search web service (not BLAST) and it returns the version of the AlphaFold database sequences that it searched, currently version 4 on the server. The current AlphaFold database version is 6 (updated Sept 2025) but k-mer search still uses the sequences from version 4. ChimeraX was trying to fetch the AFDB entry for Q9H0A0 from AFDB v4, but it does not exist in that version. The alphafold fetch command tries to fetch from v6 and it does exist in that database.

I've changed the ChimeraX code so instead of fetching AFDB entries from the version that k-mer search says it used, it searches from the current AFDB version. So alphafold match will now always try to get the AFDB entries for a uniprot identifier from the most recent database.