What's the best way to perform antibody docking using the newer Rosetta code (i.e. weekly releases) that allows for the same degrees of freedom as the older snugdock procedure (something functionally equivalent is fine). If someone has pyrosetta code or an xml RosettaScripts file, that would be most helpful.
The Rosetta3 SnugDock protocol was recently added into the weekly releases (within the last month). I don't believe it is implemented in RosettaScripts, but you can run it from the command line (the app is snugdock.<platform>) using the recommended local docking flags (https://www.rosettacommons.org/docs/latest/application_documentation/docking/docking-protocol), along with the additional flags -loops:refine_outer_cycles 3 -loops:max_inner_cycles 80 -nstruct 1000.
Thanks Nick - works great!