Prasenjit Mukherjee wrote: > I have a question for you. I have generated models for a sequence > using one structural homologue. In one set i have used 1 crystal > structure of the reference protein and generated 10 models. In the > second set i have used two crystal structures of the same reference > protein and generated 10 models.The sequence alignment is the same in > both cases. My question is, can i compare the pdf violations of a model > generated in set 1 with a model generated in set 2 ?

The energy of a model (and consequently, the violations too) is a function of your set of restraints, so if your restraints are different, any comparison of energies - or violations - can only be qualitative. Generally speaking your set of restraints (.rsr file) will be different for single template and multiple template runs - e.g. some monomodal distance restraints in the single template case will be biomodal in the multiple template case.

Ben Webb, Modeller Caretaker