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[modeller_usage] Need help with automating Modeller flow?

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,