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