I would like to refine my models of a homopentamer with loop refinement.
In the past (Mod8) I would use loopmodel, but noticed that there is an
"improved" loop modeling routine dope_loopmodel() which uses (among
other things) the DOPE score in the refinement process. In various parts
of the manual it mentions that the DOPE score was developed for
single-chain models and shouldn't be used as an evaluative tool for
multichain models. Does this also meas that the dope_loopmodel() routine
shouldn't be used for loop refinement of multichain models? What's the
downside of using it for multi-chain models?
If so, this would be a shame since there are also other enhancements
(Leonard_Jones potentials, etc.) unrelated to DOPE that would be nice to
be able to use.
Mike White