Dear Modeller users,

I'm generating diverses models to my protein (400 - is this to great?). However I don't know how is the best parameter to look when choosing the best model. Objective function from Modeller, ProCheck parameters, Energy parameters... What parameters you use and why? If using Ramachandran plot as a discriminative parameter, how great must be the parameters calculated (for example: >90% in favored regions, <1% in disalowed regions)? Any help is welcome.

Thanks for advice, Cassiano Carromeu.