Re: [modeller_usage] model_comparison

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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