I just started using PyRosetta and had a couple of questions. I am following the ligand.py script
1> What is dock_jump = 1 and movemap.set_jump(1, True)
2> Is there a way to keep the ligand in the binding pocket (PKA in the example, I noticed it was docked outside the pocket in many cases.
3> Is there a way to randomly translate / rotate just the ligand within the binding pocket?