Hi, Foldseek ran successfully with PDB but crashed in an independent comparison to AlphaFold DB (see attached). Looks like a problem with alphafold file name? Thanks for your help. Best, david David M. Miller, III, PhD Professor Cell and Developmental Biology 465 21st Avenue South PMB 407935 3120 MRB III Vanderbilt University Nashville, TN 37240-7935 (615) 343-3447 https://medschool.vanderbilt.edu/miller-lab/
Hi David, The AlphaFold database introduced isoform predictions in version 6 and these have longer database identifiers, in your case AF-Q8N9C0-2-F1-model_v6 refers to isoform 2. Older AlphaFold database versions had just one isoform and the id would look like AF-Q8N9C0-F1-model_v6 (with no -2- part). ChimeraX needs to parse these long identifiers in order to fetch them from the database and the error message you see is because it does not know about the isoforms. I'll see if I can make ChimeraX handle AlphaFold database isoform predictions. I'll send another message if I get it to work. Tom
On Feb 10, 2026, at 1:10 PM, Miller, David M via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Foldseek ran successfully with PDB but crashed in an independent comparison to AlphaFold DB (see attached). Looks like a problem with alphafold file name?
Thanks for your help.
Best, david
David M. Miller, III, PhD Professor Cell and Developmental Biology 465 21st Avenue South PMB 407935 3120 MRB III Vanderbilt University Nashville, TN 37240-7935 (615) 343-3447 https://medschool.vanderbilt.edu/miller-lab/
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Hi David, I fixed the Foldseek AlphaFold database searches to handle Uniprot isoform structures. I also made it so you can directly fetch such isoform structures using the ChimeraX menu File / Fetch by ID / AlphaFold database with an ID like Q8N9C0-2 to download the isoform 2 structure for UniProt Q8N9C0. Or you can use the ChimeraX open command open Q8N9C0-2 from alphafold These improvements will be in tonight's ChimeraX builds (dated February 10, 2026 or newer). Thanks for reporting the problem. Tom
On Feb 10, 2026, at 3:02 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi David,
The AlphaFold database introduced isoform predictions in version 6 and these have longer database identifiers, in your case AF-Q8N9C0-2-F1-model_v6 refers to isoform 2. Older AlphaFold database versions had just one isoform and the id would look like AF-Q8N9C0-F1-model_v6 (with no -2- part). ChimeraX needs to parse these long identifiers in order to fetch them from the database and the error message you see is because it does not know about the isoforms. I'll see if I can make ChimeraX handle AlphaFold database isoform predictions. I'll send another message if I get it to work.
Tom
On Feb 10, 2026, at 1:10 PM, Miller, David M via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Foldseek ran successfully with PDB but crashed in an independent comparison to AlphaFold DB (see attached). Looks like a problem with alphafold file name?
Thanks for your help.
Best, david
David M. Miller, III, PhD Professor Cell and Developmental Biology 465 21st Avenue South PMB 407935 3120 MRB III Vanderbilt University Nashville, TN 37240-7935 (615) 343-3447 https://medschool.vanderbilt.edu/miller-lab/
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participants (2)
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Miller, David M -
Tom Goddard