I'm trying to compare another method to Rosetta's side chain packing. My first pass is just using default options for the PackMover, and the results I'm getting out of Rosetta are pretty bad by comparison. Are there good rule of thumb settings for establishing a baseline over a set of proteins?
I am setting up a PackMover in C++ code, as opposed to running the command line fixbb application. Looking through the fixbb code I see the following options, some of which aren't mentioned in the documentation:
option.add( minimize_sidechains, "Do minimization of side chains after rotamer packing").def(false);
option.add( min_pack, "Pack and minimize sidechains simultaneously").def(false);
option.add( stochastic_pack, "Pack using a continuous sidechains rotamer library").def(false);
These all suggest a continuous optimization after rotamer packing, do they differ in any way? Any explanation would be helpful.