On 9/25/20 12:22 PM, Li,Haoxi wrote: > 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: https://salilab.org/modeller/9.25/manual/node497.html

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.

Ben Webb, Modeller Caretaker