Request: output MSA from already aligned structures

[gezmi]

Hi,

This is a great work and I would like to have a feature request (or please let me know how to do this if already possible).

Sometimes I do my own alignemnts, and would only like to have the MSA, based on those, without realigning. Would it be possible to input a bunch of prea-ligned structures and get the MSA? Surprisingly, no similar tools provides this feature.

My actual use-case is having protein interactions, aligned to one of the monomers which are homologues. I want to extract an alignment for the other partner of the interactions (peptides). I could do the alignment, save only the peptides' structure and input it to foldmason to get an MSA easily.

Thank you very much!

[foreveremain]

I'd suggest you look at https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html - it's pretty slow for big (or many) structures, but does the job.