Re: [modeller_usage] pir format

[Modeller Caretaker <>]

Urszula Uciechowska wrote:
> 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. 

You can certainly use FASTA format files, but we recommend PIR for most 
modeling purposes, since it holds additional information not present in 
FASTA files (e.g. the name of the PDB file for each template). You can 
find plenty of examples of PIR files in the examples and tutorial, or 
see the reference at http://salilab.org/modeller/9v2/manual/node412.html

> aln.append(file='Sirt1.ali', align_codes='Sirt1')

This line needs to be changed (by adding alignment_format='FASTA') if 
your .ali file is in FASTA format, otherwise Modeller will use PIR by 
default. See http://salilab.org/modeller/9v2/manual/node267.html

	Ben Webb, Modeller Caretaker
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