The silent file format is a Rosetta specific (trajectory) format that is used to store ensembles of structures. These are usually the final structures of a structure determination protocol but can also be structures collected from multiple runs at a certain intermediate check-point or a whole trajectory of a single run.
The ScoreFunction is a list of weights for predefined scoring terms (e.g., vdw, env, fa_atr...). The score-terms stand for a certain physical interaction whose calculation has been implemented as an energy function within Rosetta.
