On 2/2/11 7:01 AM, sankari thirumal wrote: > I would like to know what is the percentage of amino acids that has to > lie in the favoured region (only favoured region) in ramachandran plot > after modeling the protein.

I wouldn't say there's a strict cutoff above which your model should be considered "bad". However, Modeller's restraints are designed to place dihedrals in the favored regions, and our assessment scores should penalize models that have residues in disfavored regions.

Ben Webb, Modeller Caretaker