Re: [modeller_usage] External Source Sequence Alignment

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
--
modeller-care@ucsf.edu             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage