Re: [modeller_usage] importing alignment into modeller.
To: Knut J Bjuland <>
Subject: Re: [modeller_usage] importing alignment into modeller.
From: Modeller Caretaker <>
Date: Thu, 18 Feb 2010 08:56:15 -0800
Cc:
On 2/18/10 5:32 AM, Knut J Bjuland wrote:
Is there any way to import alignment created without using modeller. Do
I have to manual make a new ali file in the pir format for modeller.
Could you please calarify the how the alignment was imported into
modeller in the difficult example from http://bioinf.cs.ucl.ac.uk/psipred/
Modeller needs both sequence and structure information in order to do
comparative modeling; thus the PIR format as used by Modeller contains a
header line that maps the sequence to a matching PDB structure. A
typical alignment format (e.g. FASTA) contains only sequence
information, so there is no way to automatically add this structural
information - you will have to add the PIR header line manually, and
that was what was done for the difficult example.
As an aside, Modeller can convert FASTA format to PIR with a script
similar to
from modeller import *
e = environ()
a = alignment(e, file='my.fasta', alignment_format='FASTA')
a.write(file='my.pir', alignment_format='PIR')
Note, however, that because FASTA does not contain structural
information, each sequence in my.pir will have a simple
"sequence:::::::::" PIR header, and you'll have to go in and change this
if it corresponds to a template structure.
If, of course, your external alignment already contains the structural
information somehow, you could write your own automatic conversion, e.g.
with some Perl or Python scripting.