[modeller_usage] Need help with automating Modeller flow?

[Ashika Umanga Umagiliya <>]

Greetings all,

I come from a computer science background (only little knowledge on 
Bioinformatics) and I work on this BioInformatics application to be used 
in a research institute.

Application need a feature to model protein 3D structure from sequences 
and I decided to go with Modeller.
The application should have a simple interface (like web interface at 
http://salilab.org/modweb ) .
I went through the Basic modeling tutorial 
(http://salilab.org/modeller/tutorial/basic.html) and have several 
questions :

1) After step 1 (build_profile.py) we have to select suitable templates 
,does the selection criteria is e-value =0 ?
2) After executing 'compare.py' ,we have to select one pdb template from 
distance matrix?
How to implement this in selection logic? What criteria does 'ModWeb' 
application use? Is there any tools to select the best template using 
the distance matrix?


Best regards,
umanga