Dear Modeller Users,
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? Thank you so much!
Best wishes, Haoxi
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
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Li,Haoxi -
Modeller Caretaker