[modeller_usage] pir format

Dear Modeller users,

I am trying to use this script for my aligment. But my target sequence is in Fasta format file, can I use it also or should i convert it? Maybe someone could write me how can i get sucha a file from fasa format. thank you in advance

from modeller import *

env = environ() aln = alignment(env) mdl = model(env, file='file', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='file', atom_files='file.pdb') aln.append(file='Sirt1.ali', align_codes='Sirt1') aln.align2d() aln.write(file='file.ali', alignment_format='PIR') aln.write(file='file.pap', alignment_format='PAP')

Best Regards, Urszula Uciechowska

MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg