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.
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