If you specify a weights file using the option '-score:weights' , will that weighted scoring function be used in optimizing side chain placement? That is, does the simulated annealing algorithm incorporate the scoring function specified by '-score:weights', or is 'score:weights' only used in the final scoring of the structure AFTER side chains are placed and the designed PDB is complete?
The weights file passed to -score:weights should be used as the "default" scorefunction by all stages of Rosetta protocols which use the default weights for - for fixbb that should be all stages - both the optimization and the final scoring.
I say "protocols which use the default weights" because there are some protocols which hard code specialist weights for certain stages, and there's complexity with centroid-mode stages and scoring. But fixbb should use the passed weights file for everything.
Thanks, that was helpful.