hi, being a new user, I am facing many problems with modeller. now consider a situation in which i want to model only one particular domain/protein in a protein-protein complex, since the structure for the other domain/protein is available, but then i want to optimize the binding region of the modelled domain taking into context, the other domain as well... is it possible that i use the optimization routine of modeller for the same, only after putting both the proteins of the complex into proper interacting/binding orientation, so that energy minimization can be performed taking into context the entire complex and not just the modelled part thanks, for helping out...

sincerely.