I have been trying for some time to implement non-canonical AAs into PyRosetta. I have the params file for the residue but when it is passed on via the -extra_res_fa , pyrosetta still won't recognize it. Next to pyrosetta being able to read this AA in a pdb, I also want to mutate (canonical) AA into modified AAs (say hydroxyl group into acrylate). The mutate_residue only takes one character as an argument that corresponds to the canonical AAs, whilst a three letter argument would be preferred.
I have also thought about writing a patch for side-chain modifications but it is still unclear to me how I would be able to use this patch to mutate AAs in the sequence.
Does anyone have a solid protocol for incorporating non-canonical AAs and/or mutations involving non-canonical AAs?
Any help is appreciated, thanks!