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    That flag is only used by one of the scientific benchmarking applications (apps/benchmark/scientific/ (You can see for yourself by grepping the codebase for instances of design_contrast; it occurs only in the option system and that one executable).

    It’s implemented in that app itself, not at a level that the fixbb app can see it (apps/public/design/ So, it’s not going to work. The fixbb executable itself “knows” which options are relevant (or at least the majority of them) – look in its cc file (and perhaps its -help output) to see which ones are supposed to work.

    I’ve never used it but I think there’s a perl script for stripping fasta files from PDBs; try rosetta-3.0/BioTools/