I have a few question concerning the energy terms computed by MODELLER:
1) Can the energy of a model computed with loop-modeling be compared
to the energy of a model computed without?
2) Can the energy of a model with an additional constraint added (like
a specific distance constraint) be compared to the energy of a model without
that specific constraint?
3) What kind of energy difference can be considered to reflect a significant
difference in the quality of models?
Dan Thomas Major
Dan Thomas Major (at Dr. B. Fischer's lab)