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