On 3/22/12 10:53 AM, Zumot, Elia Nabil wrote: > Is there a way to generate a homology model using several subunits as > template? The protein I wish to model is a homotrimer. Am I wrong or > is what is explained in "Building a model from multiple templates" > not relevant here since I need the three subunits together in space > (without steric clashes).

Unless I don't understand your question, this is covered by http://salilab.org/modeller/9.10/manual/node28.html

Modeller is not going to magically determine the interface region between your subunits and dock them, of course. You need to give it information about the interface between subunits (either by giving it a multimeric template, or by supplying it with subunit-subunit restraints if you only have monomeric templates).

Ben Webb, Modeller Caretaker