Hope this email finds you well! I have a question about building
homology models with sequence alignments coming from external sources
(BLAST, PROMALS3D, etc). Since PIR format alignment files are usually
not provided by these sources, do I need to manually construct the
file based on the alignment I have? Are there any other ways?
If you have templates in this alignment, you would need to add a PIR
header to tell Modeller which range of ATOM/HETATM records in the
PDB/mmCIF file correspond to the sequence:
You would probably need to do that manually. If you are sure the
sequence matches, you can put a dot "." for every residue number and
chain ID, and Modeller will make a best effort to match your sequence
against that in the PDB file to automatically determine the range.