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steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
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Problem about K-mer #134

Closed yang-nei closed 1 year ago

yang-nei commented 1 year ago
截圖 2023-05-18 下午5 46 37

Hi there! I try to blast structure to databases being set by myself , However I faced some problem about "No k-mer could be extracted " and I'm sure my sequences length is more than 14 residues. How shell I do?

milot-mirdita commented 1 year ago

There is something wrong with your pdb tgz files. Foldseek does not find any structures insides. See the ignored 0 out of 0 line.

yang-nei commented 1 year ago

Thanks ! I've resolve the problems that set up my own databases by put in a lot of pdb. and cancel the tgz. file, however I got another questions about I can't search mutilple pdb. by one time( I've tried to use "foldseek easy-search (a lot of pdbs) fasta. tmp " but only showing the result which the first one I threw-in in output format )

martin-steinegger commented 1 year ago

To search multiple PDBs try this: 

foldseek easy-search queryPdbFolder/ pdb_db aln tmp