Hi all,
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?
2) Is it a good idea to model several loops (say 10) at the same time?
Any help will be appreciated.
Yours, Mehdi
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
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Mehdi Bagheri-Hamaneh -
Modeller Caretaker