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