saccenti@cerm.unifi.it wrote: > I want to model a complex A1+B1 on a template complex A+B where A and B > are proteins. I have only one template available. > > Does somebody as a warking script to do this?

Building multi-chain models should be exactly the same as regular single chain models - just add chain breaks (/) to your alignment where necessary. There's an example at http://salilab.org/modeller/9v2/manual/node28.html although that does more than you probably need (unless A and B are identical, you probably want to remove the symmetry restraints used in that example).

Ben Webb, Modeller Caretaker