Martin Steinegger

@Old-Shatterhand is it possible for you to share your example?

Thank you so much for this blazing fast. @Old-Shatterhand cool project! :) @mrauha we do not have a way to get unique pairs. cigar/qaln/taln is all from TM-align if you...

I consider this resolved for now. Please reopen if you still have issues.

We have recently added the `--format-mode 5` option to our software, which generates PDB files with all Calpha atoms superimposed based on the aligned coordinates.

Should be working now.

The most current version should have this format output flag.

This is hopefully solved now with our much faster Foldseek TMalign search workflow.

I consider this issue closed. If the error still persists in the newest version, please reopen it.

Does this still persist?

Yes, short peptides tend not to yield reliable E-values. Since Foldseek generates local alignments, it is possible for structural fragments of only five residues in length to appear by chance...