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.