AddHelixSequenceConstraints Mover

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    • May 30, 2019 at 10:17 am #3163
      Anonymous

        Hello all

        I want to design interface of a complex which contains only alpha helices ( has not any betta strand) , it is important for me that the secondary structures of alpha helices would not be disturbed during sequence design.

        Recently I have found a suitable mover  ‘”AddHelixSequenceConstraints Mover” https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/best_practices/AddHelixSequenceConstraintsMover.

         I think by using this mover during interface design  some constraint in sequence design cause to preserve the secondary structure of  alpha helices during design

        Now I have two questions first does this mover do what I want? 

        and second, did I add this mover to my script in the correct place? would I add or edit something in my script ? I have attached my script here

      • June 13, 2019 at 9:57 pm #14768
        Anonymous

          This mover will bias design towards sequences that favour helices at any position that is in a helix.  So in that sense, yes, I think it will do what you want.

          You’ve added it in the correct place, and have set up a scoring function correctly, but you’re not passing that scoring function to the PackRotamersMover that will do the actual design.  You need to change the PackRotamersMover setup to be:

          <PackRotamersMover name=”packrot” scorefxn=”tala_comp” task_operations=”design,cmdline”/>

        • June 13, 2019 at 9:59 pm #14769
          Anonymous

            (One other note: if you want to use the talaris2014 scoring function, which is a legacy scoring function, be sure to run Rosetta with the -restore_talaris_behavior flag.  I’d recommend using the new default, ref2015, though, in which case you don’t need any flags, but you do need to change talaris2014.wts to ref2015.wts.)

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