I just downloaded and installed Rosetta 3, and was hoping to use the Holes functionality. I can't seem to find any documentation on it yet (as far as I've looked). When I looked through the files, I could locate the source files compute_holes_score.cc(hh) under Scoring, but was not sure if it has been included in the build process or not.
Can someone tell me how I could use the Holes functionality? TIA.
Looks like Will decided not to release that with 3.0 in February. I assume it's planned for 3.1 (which is supposed to be soon).
The low-level stuff (the scoring stuff you found) is still there, but the executeable level stuff was removed from the code before release for whatever reason. I don't know enough about the low-level bits to tell you how to use them. I can tell you that "rosettaholes" and "packstat" are the same thing.
tangentially related but is there also a flexible backbone design application planned for 3.1? There was such functionality in Rosetta++ if I remember correctly. I am currently running fixbb/relax cycles but not sure if this is the best way to do flexible backbone design.
There are multiple flexible backbone design applications under development. Nobody knows what the best way is yet, so don't feel lost in the woods. I don't think anyone is planning on releasing with 3.1. (I think cycles of design and relax may have been what was in ++ anyway, for what it's worth).