The -symmetry:perturb_rigid_body_dofs flag

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  • This topic has 2 replies, 2 voices, and was last updated 12 years ago by Anonymous.
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    • #1259
      Anonymous

        Hi,
        I am working on symmetric docking in rosetta3.2. I want to add the -symmetry:perturb_rigid_body_dofs flag to my docking , however it says in the manual that it gets ANGSTROMS and then DEGREES as arguments.As this flag is similar to the -docking:dock_pert flag from non-symmetric docking in rosetta3.1 where the arguments order is then , I wander if the arguments order in -symmetry:perturb_rigid_body_dofs is also then and maybe there have been a mistake in the manual of rosetta3.2 regarding this symmetric docking flag arguments order. What is the correct order of the arguments then for the -symmetry:perturb_rigid_body_dofs flag ?
        Also, what are the recommended default values for the ANGSTROMS and DEGREES given to -symmetry:perturb_rigid_body_dofs, are they 8A and 3Deg (same as in -docking:dock_pert)?

        Thank you,
        Doran

      • #7046
        Anonymous

          The order is correct in the manual (ANGSTROM DEGREES). This is the same as for heterodimeric docking (http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_docking.html). The recommended values for heterodimeric docking would work ok also for symmetric docking (3A and 8Deg). However, this may vary depending on what you are trying to do and what symmetry you use.

        • #7048
          Anonymous

            Thank you very much.
            Doran

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