Re: [modeller_usage] total of DOPE per residues not equal to global DOPE?

[Modeller Caretaker <>]

hori koshii wrote:
> Hi, I have tried to add up all the DOPE score per residue but the value 
> is not equal to the global DOPE score at all. Anyone knows the answer 
> please?

I'm assuming by "DOPE score per residue" that you're making an energy 
profile with a script similar to the last one shown in the basic 
tutorial at http://salilab.org/modeller/tutorial/basic.html

The sum over all residues will not generally match the total energy due 
to two factors - normalization and smoothing. The first (controlled by 
the normalize_profile argument) "normalizes" the score per residue by 
dividing the score by the number of restraints on that residue. The 
second (controlled by smoothing_window) smooths the score per residue by 
window averaging.

If normalize_profile = False and smoothing_window = 0, the two numbers 
should be very similar.

	Ben Webb, Modeller Caretaker
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