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



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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