I use standard KIC script for a loop modeling by PyRosetta. However in some cases the generated loops do not have appropriate structures, especially in the middle of the loop, were the cut point is. Typically, I get loops with a good structures, however in several cases the loops have a bad chemical connections or even broken structures in the middle of these loops.
I wanted to filter out these structures using Rosetta standard scoring function, but all scores for bad structures are in the same range or even better than the energy for good structures.
It is difficult to explain why standard scoring function doesn’t work in that case?
I am looking for any explanatory ideas how to filter out bad structures from good one using Rosetta scoring function (or functions)?
Thank you, Victor