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