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

On 04/20/2015 03:39 AM, vipul AT 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
--
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage