Thanks for the reply, Troubling you with one more query though....

"PIR files are just plain text, so they're very easy to make manually in a text editor or with some simple scripting."

I have read in the forum that one needs to input PDB structure details also while changing the format, Please let me know if this is required for query sequence also or only while submitting the alignment as input (changed to PIR).

Thanks and Regards,

Nanda

On Fri, Sep 21, 2012 at 6:00 PM, Modeller Caretaker <modeller-care@salilab.org> wrote:

On 9/21/12 6:26 AM, Nanda Pandey wrote:

Do i need to convert my sequence to PIR file format in order to use it.

If by "use it", you mean you want to build a comparative model, then yes.

If yes, how do i do it??

PIR files are just plain text, so they're very easy to make manually in a text editor or with some simple scripting.

Is it recommended to generate alignment from external sources and then
perform modelling using modeller or I can generate my model for a
sequence using only modeller.

You can do it either way. The alignment you use for modeling doesn't have to be generated by Modeller.

Ben Webb, Modeller Caretaker
--
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