RosettaScripts – SetupNCS mover

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    • March 25, 2016 at 7:42 pm #2397
      Anonymous

        Dear all

        I was trying to mix ligand docking with protein design of a symmetric dimer by using the SetupNCS mover. I still don’t know why the mover is not being used…the resultant pdbs were modified at the sequence level but both chains are different.

        thanks in advance

        felipet

         

        The script used is:

         

                <MOVERS>

                        <SetupNCS name=ncs bb=1 chi=1 symmetric_sequence=1>

                              <NCSend source=”115B-227B” target=”1A-113A”/>

                              <NCSend source=”1A-113A” target=”115B-227B”/>

                        </SetupNCS>

                        <Translate name=translate chain=X distribution=uniform angstroms=0.25 cycles=50/>

                        <Rotate name=rotate chain=X distribution=uniform degrees=360 cycles=500/>

                        <EnzRepackMinimize name=desmin design=1 repack_only=0 scorefxn_minimize=myscore scorefxn_repack=soft_rep minimize_rb=1 minimize_sc=1 minimize_bb=0 cycles=2 minimize_lig=1 min_in_stages=0 backrub=0 task_operations=liginter/>

                </MOVERS>

                <PROTOCOLS>

                        <Add mover_name=ncs/>

                        <Add mover_name=translate/>

                        <Add mover_name=rotate/>

                        <Add mover_name=desmin/>

                </PROTOCOLS>

         

      • March 26, 2016 at 5:31 pm #11491
        Anonymous

          I realize now that it will symmetrize my dimer, but it is not what I was thinking…do you have any suggestion?

          thanks

          felipet

        • April 29, 2016 at 3:26 pm #11550
          Anonymous

            Unlike normal symmetry which enforces an obligate symmetry in the modification itself,  the non-crystallographic symmetry mover enforces the symmetry via energetic restraints on the deviations between the residues. This means that in order to acutally apply the symmetry between the subunits, you need to be using a scorefunction which applies the energetic penalty while moving/designing.

            Unfortunately, the default scorefunction does not have the appropriate energy terms turned on. What you’ll want to do is to turn on (set to 1.0 or maybe more) the “res_type_constraint” weight in your “myscore” and “soft_rep” energy functions. (Add the dihedral_constraint term too, if you want the structure to be maintained as symmetric as well as the identity.)

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