> hello everybody, > i am tryong to model the structure of enzyme which is crosslinked > homodimeric protein > two identical chains of protein are crosslinked in opposite orientation > to form the two compete active sites. > that is, both chains contribute fo the foramtion of aech of the active > site. (there are 64 hydrogen bonds involved in inetaction between two > chains) > i tried to model to chains seperatly and superimpossed bsed on template, > but the orientation of the chains is not giving the proper active site, so > how i can model the whole protein, i.e. both the chains simultaneously > so that i can get full active site? > or is there any way by which seperatly modeled chaines can be put together? > please suggest any solution for this problem.

It is straightforward to model both chains together - just add a chain break (/) to your alignment. See http://salilab.org/modeller/9v1/manual/node27.html for an example. (That example also constrains the two chains to be symmetrical, but you don't have to do that, of course.)

Ben Webb, Modeller Caretaker