On 8/7/12 5:08 AM, Nanda Pandey wrote: > I am very new to modeller so a small query, Please let me know how do I > compare the template sequences using compare script. Do I need to > download individual template files from PDB

Yes, you will need to download template PDB files.

> Also, whta should be done in case I have too many template > sequences with same e -value (e.g. 0 e -value) should i download all of > them??

You can if you like - how you choose which template(s) to use for modeling is up to you.

Ben Webb, Modeller Caretaker