Re: [modeller_usage] scoring of the full loop-models

[Modeller Caretaker <>]

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
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