Danny Diaz comments

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                                            Danny Diaz

Unable to process assembly cif files that have 2 and 3 character auth_asym_ids

So we are still unable to write out cif files. It seems like the error is in the `freesasa_node_atom_chain` function, which queries the `atom properties` struct for the chain id....

Unable to process assembly cif files that have 2 and 3 character auth_asym_ids

I think you should set up a pull request for this issue with the current commit you shared. I'll see if I can also take a hack at this when...

Issue with Cb atoms of threonines, perhaps other amino-acids?

I reviewed your output files and it looks like the model collapses Ca and Cb atoms for these amino acids, which prevents PyMol from properly visualizing them. Not sure if...

Run MMSeqs/FoldSeek with sequences that do not use amino acid sequences

Secondary Structure alphabet from STRIDE. So 8 letters. Do you think this is easily doable? Sorry we didn't get to meet up in Vancouver!

Run MMSeqs/FoldSeek with sequences that do not use amino acid sequences

If you could provide me some instructions on how to implement what is needed I would be happy to help.

Segmentation fault when using --allow-deletion with result2msa

Essentially, if you could help me figure out how to output an a3m file where the query sequence is in the `qaln` format and the aligned sequences are in the...

Segmentation fault when using --allow-deletion with result2msa

Is this also true for —allow-deletions in MMSeqs2? Or just foldseek? Yeah we just remove the lowercase letters or do 1-1 alignments to have indels in both the query and...