On 7/10/22 11:15 PM, Li Xue via modeller_usage wrote:
I am trying to refine a loop in a multi-chain complex. During the
refinement/remodelling phase of the loop, does modeller molPDF include
non-bonded energies between chains? Or it will only include the
energies within the loop?
First, the loop is optimized without considering interactions with the
rest of the system, then a second round of optimization is done which
also includes all loop-nonloop interactions.
If you're asking whether the score includes interactions between nonloop
atoms in different chains then no, it does not. Only loop atoms are
moved during optimization, so any nonloop-nonloop interaction will be
constant and so can be ignored. If for some reason you want to include
that score (remember, the molpdf is essentially useless for model
assessment) then use Selection.energy() to score the final model.