Nicky Thrupp wrote: > I am building a protein with four chains (based on a tetrameric > template). I was wondering about the algorithms that Modeller uses - > does it build all four chains simultaneously, or does it build them one > at a time? I am worried about steric clashes if the chains are built > indiviudally and then put together afterwards.

All four chains are built simultaneously, so you should not have any trouble with steric clashes.

Ben Webb, Modeller Caretaker