i am looking for the functionality of "-favor_native_residue" (add a energy penality favoring/disfavoring the native residue) from rosetta2.3 in rosetta3.x. I found a command line flag in 3.4 "-favor_native_res". fixbb.linuxgccrelease accepts the flag without complaining, but I have the feeling he does not used it properly: e.g. I set an quite high value of -4 REU, but the mutations look roughly like w/o the flag set. Can it be that the parser reads it but the functionality is not implemented in fixbb? Greping in 3.4 for "favor_native_res" I find it mostly in the context of enzdes. Any idea how to get this functionality into fixbb design, one options seems to be RosettaScripts. What's about PyRosetta does anybody know how to directly feed favor_native into the PackRotamer mover?
Thanks a lot!