On 4/16/19 4:28 AM, malkeet singh Bahia wrote: > In the loop refinement process, is the DOPE score reported only for the > refined region or full protein model?
Neither. It is the score for the refined region interacting with the entire model. DOPE is a pairwise atomistic score, so it is evaluated for all nearby pairs of atoms where at least one atom is in the refined region.
> If only for the refined region, is > there any 'python code', which could be clubbed with loop refinement > script to report the DOPE scores of the complete protein models as well?
This shouldn't be necessary, since DOPE scores are only reliable for ranking, and since the non-refined parts of the system don't move, the contributions to the score from the non-refined-non-refined atom pairs should be constant, so the rankings won't change. But sure, you can call assess_dope directly on whatever selection you like: https://salilab.org/modeller/9.21/manual/node258.html
If you want to tie this in to loopmodel automatically, you can write a little function to do it and assign that function to loop_assess_methods in the usual fashion. See modlib/modeller/automodel/assess.py for the existing (very simple) functions.
Ben Webb, Modeller Caretaker