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Re: [modeller_usage] loop modeling

Mehdi Bagheri-Hamaneh wrote:

I am very new to loop modelling using MODELLER. I have been reading the
documentation to find the answer to my questions, but I didn't find
anything. I have two questions about loop refinement:

1) How can refine more than one loop at the same time. I know how to
model one loop, but how can I select more than one region to refine?


See http://salilab.org/modeller/manual/node32.html


2) Is it a good idea to model several loops (say 10) at the same time?
10 is a lot of loops, so you will probably have to build many models to stand a chance of sampling the best conformation of them all. See also http://salilab.org/archives/modeller_usage/2006/msg00251.html 

	Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
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