[modeller_usage] Building a model from multiple templates ?

[Ashika Umanga Umagiliya <>]

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.

Is this process correct?

Thanks in advance.
Umanga