Chido Mpamhanga wrote: > I'm new with modeller, I have used it to do simple models.. However I'm > now trying to model a tri-metric complex where the active site of the > complex is includes all three subunits. How do i go about this?

Building multi-chain models is straightforward, particularly if you have a multimeric template - just add chain breaks ('/') to your alignment where needed. See the example in the manual: http://salilab.org/modeller/9v3/manual/node28.html

If you have ligands which interact with two or more chains, Modeller should handle them correctly, as the constraints are distance-based, not sequence-based.

Ben Webb, Modeller Caretaker