Re: [modeller_usage] How to go about refinement of multiple loops in a protein model?

On 04/20/2015 03:39 AM, vipul@nccs.res.in wrote: > I have the following doubts and questions: > Do I need to refine all of these three loops?

No, only if you think it'll be useful.

> and should there be an order > in which to refine each of these loops ( i mean, starting from N-terminus > of the larger loop, etc)?

Usually it's best to refine all three simultaneously.

> Do small loops (1-5 residues) need to be refined only by the modeller > script 'model-loop-tiny.py'? If yes, please explain, why? Or the regular > 'loop.py' script is fine?

Use the regular loop.py script.

Ben Webb, Modeller Caretaker