Re: [modeller_usage] Question about DOPE

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

Wei Chen wrote:
> I read something about DOPE. I understand it is a statistical potential. 
> I followed tutorials to calculate the DOPE profile. Someone said that 
> DOPE profile is calculted by Potential Energy / Restriction. In the 
> tutorial, it seems that DOPE profile should be above - 0.03. My question 
> is why it shoud be above -0.03. Why is the potential energy positive if 
> it is above -0.03?

The profile, just like the DOPE score itself, is just an energy measure 
(the profile shown in the tutorial is energy/number of restraints, for 
each residue). Thus, it is not normalized, and any cutoff you choose is 
arbitrary.

	Ben Webb, Modeller Caretaker
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