I cannot get -design_contrast to work with fixbb design. I have included the flag with a filename to output to (e.g. -design_contrast contrast.file) and without a file (e.g. -design_contrast). Neither works, there is not file generated that I can find. Can anyone help me with this?
That flag is only used by one of the scientific benchmarking applications (apps/benchmark/scientific/design_contrast_and_statistic.cc). (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/fixbb.cc). 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/getFastaFromCoords.pl.