Re: [modeller_usage] Building a model from multiple templates ?
To:
Subject: Re: [modeller_usage] Building a model from multiple templates ?
From: Ashika Umanga Umagiliya <>
Date: Thu, 05 Feb 2009 18:47:51 +0900
Sorry for that, I saw the correct procedure in Advanced tutorial !
Ashika Umanga Umagiliya wrote:
Greetings ,
After went through the Basic tutorial , I wanted to build a model from
multiple templates (as shown at
http://www.salilab.org/modeller/manual/node21.html)
For that it says "-- simply provide an alignment between all of the
templates and..."
So to create the alignment between all of the templates,I modified the
script "align2d.py" of step 3 (Aligning TvLDF with the template) in
Basic tutorial , as follows:
-------------------------------------------------------------
from modeller import *
env = environ()
aln = alignment(env)
#modified from here to add several templates
#template 1
mdl = model(env, file='1bdm', model_segment=('FIRST:A','LAST:A'))
aln.append_model(mdl, align_codes='1bdmA', atom_files='1bdm.pdb')
#template 2
mdl = model(env, file='1b8p', model_segment=('FIRST:A','LAST:A'))
aln.append_model(mdl, align_codes='1b8pA', atom_files='1b8p.pdb')
#template 3...
#template 4...
aln.append(file='TvLDH.ali', align_codes='TvLDH')
aln.align2d()
aln.write(file='TvLDH-mult.ali', alignment_format='PIR')
aln.write(file='TvLDH-mult.pap', alignment_format='PAP')
-------------------------------------------------------------
Then using the generated "TvLDH-mult.ali" file I am going to do the
automdelling with multiple templates.