Sridhar Acharya wrote:
I want to know what rotameric state of the mutant residues that the MUTATE_MODEL option of MODELLER generates? What rotameric configuration does the program generates. Is it the most optimum that is possible for the model or is it generated based on some other scoring scheme?Is there any control on the rotameric state of the mutant residue.
The model.mutate() command itself only changes the internal residue type, and doesn't affect the structure at all. If you use the script in the wiki (http://salilab.org/modeller/wiki/Mutate_model) then it is followed by generate_topology() and build(), which generate the structure of the mutant from the CHARMM internal coordinates. This will not be the optimum rotamer since it does not take the rest of the structure into account. Then some optimization is done to yield an optimum configuration.
Ben Webb, Modeller Caretaker
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