I have a huge database of PDB files and I need to calculate their RG along with their energy(any relevant scoring).
Earlier version of Rosetta had RG_Energy.cc and RG_Energy_Fast.cc type of files which did this kind of job.
Is there something similar for Rosetta3.4 ?
Generally speaking, one activates alternate scoring methods by setting their scorefunction weights to a nonzero number. The simplest way to add a term for scoring to copy the scorefunction you want (database/scoring/weights/), add the term you want with a nonzero weight, and then pass the new weights file to -score:weights. This should work with score_jd2 but I’ve never tried. The scorefunction term name for radius of gyration is “rg”, so “rg=1.0” will turn it on with a weight of 1.