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