Recently I started attempting to use PyRosetta to perform protein-protein docking. I was following the PyRosetta docking tutorial at www.pyrosetta.org/tutorials and managed to get a script together that can generate a bunch of coarse models and then the best n of them are submitted to high resolution refined docking. I was interested in attempting to set up constraints for these docking experiments, so I generated some constraints files that include AtomPair and/or Site constraints but I'm not sure how to use these easily in PyRosetta. I discovered that I have to import rosetta.core.scoring.constraints to get access to a lot of useful functions, one of which is "add_constraints_from_cmdline_to_pose" so I can specify the constraints file in init's "extra_options" argument. That seems to work. But I tried to use add_constraints_from_cmdline_to_scorefxn on a scoring function but it doesn't appear to add weights for atom_pair and site constraints. Is there a special weights file for docking (was using "interchain_cen" for lowres and generally "talaris2013" for highres) that includes these weights so I don't have to guess what they should be, or is there a way to "turn on" these constraints in a pre-existing scoring function?
I know this is the PyRosetta forum, so this may not be an appropriate place to ask this, but if I use the regular Rosetta docking_protocol to do this, do I just specify the constraints file on the command line and then the constraints will be used properly (so I don't have to fiddle with score function options)? It seems that in the PyRosetta tutorial you run a large number of lowres docking simulations followed by a smaller amount of highres simulations on the best lowres models (if I have understood the tutorial correctly). How do you do this in regular Rosetta? Is it just specifying an nstruct value and each struct is the result of a lowres followed by highres simulation?
Thank you for your assistance and I apologize if these are basic questions that were answered elsewhere.