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?