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 > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >