Hi Matthias, Elaine, Foldseek is a structure-based search, in other words it uses the atom positions. So just deleting the structure residues will restrict what Foldseek uses to the residues with atom coordinates. As far as I know Foldseek makes no use of residues listed in the sequence that do not have coordinates, so it is not necessary to change the sequence information in the structure file to use Foldseek on a trimmed down structure. Tom
On Jan 28, 2025, at 1:15 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Matthias, Regarding limiting the foldseek query to a part of a chain:
The full sequence is still in the metadata of the chain even though you delete some of the atomic coordinates.
To only search with part of a chain, one (somewhat tedious) way is to delete the rest of the chain, save as PDB, text-edit the PDB file to remove all the SEQRES records, open the PDB file, use foldseek search.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/foldseek.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 28, 2025, at 1:00 PM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Just checked It out, what a great tool!! In my specific case I was interested to search only a small domain/short linear motif present in my POI - from what I saw, foldseek always searches the entire chain? I thought I could simply delete the residues I am not interested in from the model prior to performing Foldseek, but this throws an error: Foldseek query failed: unsupported operand type(s) for /: 'str' and 'int'. Are there other ways to search only a selection of my model?
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