On 12/16/2010 11:51 AM, Starr Hazard wrote: > This is several questions I guess. 1) Are DOPE energies normally > distributed? Could I statistically compare DOPE scores of models made > with one template to those from another template.
DOPE is a sum of individual energies over all pairs of atoms in your final model - it does not include any information from the template or modeling process. So you can compare DOPE scores for two models of the same sequence, regardless of their source.
> 2) I have some evidence that longer XY pairs have "better" DOPE > scores than shorter pairs. Is there a statistical way to control for > "length"?
You can't compare these directly. Use the normalized DOPE score instead, which *is* corrected for length (it is a z score).
> 3) I was just looking at DOPE scores for two models. One with from an > alignment with gaps and the other from an alignment without gaps. > The PDB model files are different sizes yet the scores are identical. > Does DOPE ignore regions that are not in the template?
Yes. See (1) above.
Ben Webb, Modeller Caretaker