On 3/23/23 5:51 AM, Isabel Elliott via modeller_usage wrote: > I am generating and refining models using the LoopModel or DOPELoopModel > or DOPEHRLoopModel methods. Sometimes I get negative molpdf values for > some of my generated models. What does this mean? I thought that the > molpdf should be positive. The models with the most negative molpdf > correspond to the most negative (i.e the lowest) DOPE scores - are these > therefore the best models?

Scores can be positive or negative; there is nothing special about a negative score. Otherwise you are right - lower scores are better.

Ben Webb, Modeller Caretaker