small molecule docking

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    • August 2, 2010 at 9:57 pm #645
      Anonymous

        Hi,
        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?

        Thanks,
        Sharang

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