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Re: [modeller_usage] External Source Sequence Alignment

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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