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