I have generated several models with different template combinations and
want select the best with regard to some regions of interest (i.e. the
ATP binding site).
In the case of the binding site my residue selection is not contiguous
(roughly all residues within 10 A. from the ATP). Does the resulting
score make sense?
What you are calculating here looks from your script to be the raw DOPE
score, not a z-score. A z-score would probably not make sense here
(because the parameterization was done with whole proteins) but the raw
DOPE score should be fine since it is just a summation over individual
atom pairs. Note however that because you are excluding some parts of
your system the scores will not reflect any "problems" (e.g. steric
clashes) in the excluded regions.