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I am doing a basic modelling following the instructions here. But different target / template sequences.

http://salilab.org/modeller/tutorial/basic.html

Do I need to convert the FASTA to PIR with a script something like this

http://salilab.org/archives/modeller_usage/2010/msg00072.html

or in the 3rd step in basic tutorial

from modeller import *
env = environ()
aln = alignment(env)
mdl = model(env, file='1bdm', model_segment=('FIRST:A','LAST:A'))
aln.append_model(mdl, align_codes='1bdmA', atom_files='1bdm.pdb')
aln.append(file='TvLDH.ali', align_codes='TvLDH')
aln.align2d()
aln.write(file='TvLDH-1bdmA.ali', alignment_format='PIR')
aln.write(file='TvLDH-1bdmA.pap', alignment_format='PAP')

Changing alignment_format='PIR' to alignment_format='FASTA' is sufficient enough?

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3  
From the second link you posted, it looks like simply changing the line of code will not work -- in the caretaker's message, it sounds like it needs to have the empty header information. However, why don't you try it both ways and report back if both give the same result? –  dd3 May 13 '13 at 22:02
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