Re: [modeller_usage] evaluation of a region with DOPE z-score

[Modeller Caretaker <>]

On 04/09/2010 06:31 AM, Thomas Evangelidis wrote:
> 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.

As for your other question, I think Jan covered that already.

	Ben Webb, Modeller Caretaker
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