Your question is answered in the FAQs:

http://salilab.org/modeller/FAQ.html#17

use that code to get the sequence from .pdb (as MODELLER reads it), and realign it with the rest of your sequences to generate a new .pir file. Otherwise just align it with the original sequence to spot discrepancies.

Tom

2010/4/12 piyush diyora <yellow_piyu46@yahoo.co.in>

Hi,
I am new to modeller.
Before building a model, we have to first modify the sequence present in the PIR file. PDB file and PIR file may have few different sequences. So is there any way or software which can align both the sequences (from PDB file and PIR file) so that the sequence present in PIR can be modified.

Thank you,
Piyush Diyora

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