Martin Steinegger

@genomewalker we will have a discussion about this issue tomorrow. We will update this issues once we have a solution.

3Di is in `pdb_ss`, `ss` stands for structural sequence.

Its a `\0` byte that sperate entries. One easy way to get rid of the null bytes would be to convert it to a tsv ``` foldseek prefixid pdb_ss pdb_ss.tsv...

We did not test MPI yet. I would for now not recommend using it!

Also, it is often better to mask the 3Di sequence instead of trimming the structure by replacing all residues to be masked with X's (X is a state that matches...

Thank you for providing such a detailed report. It seems that through the cutting, the last 3di state changes from V to D. D and V have a negative substitution...

This should be now available in our newest release: https://github.com/soedinglab/MMseqs2/releases/tag/14-7e284

This should be now available in our newest release: https://github.com/soedinglab/MMseqs2/releases/tag/14-7e284

@shelkmike what do you try todo? Knowing your use-case would help us to guide what tool to use.

@milot-mirdita could you help with this?