On 12/7/16 3:47 AM, ncuspywangxuedong wrote: > I was using modeller in order to obtain a model satisfying crosslink > restrains. > Now I know the crosslinked sites, but I do not know how to > add crosslink restrains. > Could you tell me how to do it? It is best If you can give specific > examples to me!

It is straightforward to add simple distance restraints to your model. There's an example adding a simple harmonic restraint in the manual: https://salilab.org/modeller/9.17/manual/node28.html

For a crosslink you probably want an upper bound restraint though: https://salilab.org/modeller/9.17/manual/node108.html

Ben Webb, Modeller Caretaker