Changing the Number of Cycles of D110_DNA_interface.py Script

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    • October 24, 2016 at 6:33 pm #2527
      Anonymous

        Hello,

        I am trying to create docking poses using D110_DNA_interface.py.  For my application I do not need extremely accurate poses (RMSD<0.5) to be created, is there anyway to limit the number of cycles the scripts runs through to create a pose? Ideally, I want to create poses in the range of RMSD between 1-20 angstroms. 

        I tried using the “Custom docking” commands in the same sample script to change the number of cycles but get the following error:

        AttributeError: ‘DockMCMCycle’ object has no attribute ‘get’.

        Thank you!

      • November 14, 2016 at 9:56 pm #11952
        Anonymous

          With the DockMCMProtocol object there are a few options you can change to change how extensively it samples: http://graylab.jhu.edu/PyRosetta.documentation/rosetta.protocols.docking.html#DockMCMProtocol

          In particular, you can use the set_first_cycle() and set_second_cycle() methods to adjust the number of cycles of the DockMCMCycle mover. The defaults are 4 and 45, respectively.

          There’s also some setup and post-docking minimization steps which are done. If you’re uninterested in this, you can simply use the DockMCMCycle mover directly. (This is what the “Custom Docking” section is doing.) . .. You may need to call dock_mcm.init_mc(pose) before running it.  

          I’m not quite sure why you’re getting the error with “get” – what’s the exact command that’s being run before that error? (You may want to manually step through the protocol on the interactive terminal to see where it happens.)

           

           

           

        • November 14, 2016 at 9:56 pm #12473
          Anonymous

            With the DockMCMProtocol object there are a few options you can change to change how extensively it samples: http://graylab.jhu.edu/PyRosetta.documentation/rosetta.protocols.docking.html#DockMCMProtocol

            In particular, you can use the set_first_cycle() and set_second_cycle() methods to adjust the number of cycles of the DockMCMCycle mover. The defaults are 4 and 45, respectively.

            There’s also some setup and post-docking minimization steps which are done. If you’re uninterested in this, you can simply use the DockMCMCycle mover directly. (This is what the “Custom Docking” section is doing.) . .. You may need to call dock_mcm.init_mc(pose) before running it.  

            I’m not quite sure why you’re getting the error with “get” – what’s the exact command that’s being run before that error? (You may want to manually step through the protocol on the interactive terminal to see where it happens.)

             

             

             

          • November 14, 2016 at 9:56 pm #12994
            Anonymous

              With the DockMCMProtocol object there are a few options you can change to change how extensively it samples: http://graylab.jhu.edu/PyRosetta.documentation/rosetta.protocols.docking.html#DockMCMProtocol

              In particular, you can use the set_first_cycle() and set_second_cycle() methods to adjust the number of cycles of the DockMCMCycle mover. The defaults are 4 and 45, respectively.

              There’s also some setup and post-docking minimization steps which are done. If you’re uninterested in this, you can simply use the DockMCMCycle mover directly. (This is what the “Custom Docking” section is doing.) . .. You may need to call dock_mcm.init_mc(pose) before running it.  

              I’m not quite sure why you’re getting the error with “get” – what’s the exact command that’s being run before that error? (You may want to manually step through the protocol on the interactive terminal to see where it happens.)

               

               

               

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