I have 2 questions regarding the high resolution stage of the symmetric docking application in rosetta3.2:
1. What exactly are the changes performed to the structure by the docking_local_refine flag (The reason I am asking this is that I want to know which clustering radius to use on the outputs and since I don’t use the perturb_rigid_body_dofs flag in this stage I don’t know how to set the radius for this clustering)?
2. In the symmetric docking application in rosetta3.2 , I could’t understand if the high resolution stage that uses the docking_local_refine flag , yields homomultimers in which each subunit has the exact same positioning of the side chains or is a-symmetry of the side chains in each subunit is allowed here?
My understanding of the symmetry code in general is that all asymmetries are forbidden; sidechains will pack symmetrically.
docking_local_refine generally tells the code not to do any coarse-grained centroid modeling and do only atomic-resolution refinement of structures, but more specifically than that it will depend on what flags you’ve used.