Fixing certain residues during refinement

[Anonymous]

Hello I’m simply wondering how I can tell Rosetta to not move residue 80-200, for example, while doing the following refinement. Thanks for any and all help!

Refinement Script:

<ROSETTASCRIPTS>

   <SCOREFXNS>

      <ScoreFunction name=”cen” weights=”score4_smooth_cart”>

         <Reweight scoretype=”elec_dens_fast” weight=”20″/>

      </ScoreFunction>

      <ScoreFunction name=”dens_soft” weights=”beta_soft”>

         <Reweight scoretype=”cart_bonded” weight=”0.5″/>

         <Reweight scoretype=”pro_close” weight=”0.0″/>

         <Reweight scoretype=”elec_dens_fast” weight=”%%denswt%%”/>

      </ScoreFunction>

      <ScoreFunction name=”dens” weights=”beta_cart”>

         <Reweight scoretype=”elec_dens_fast” weight=”%%denswt%%”/>

         <Set scale_sc_dens_byres=”R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88″/>

      </ScoreFunction>

   </SCOREFXNS>

   <MOVERS>

      <SetupForDensityScoring name=”setupdens”/>

      <LoadDensityMap name=”loaddens” mapfile=”%%map%%”/>

      <SwitchResidueTypeSetMover name=”tocen” set=”centroid”/>

      <MinMover name=”cenmin” scorefxn=”cen” type=”lbfgs_armijo_nonmonotone”

         max_iter=”200″ tolerance=”0.00001″ bb=”1″ chi=”1″ jump=”ALL”/>

      <CartesianSampler name=”cen5_50″ automode_scorecut=”-0.5″ scorefxn=”cen”

         mcscorefxn=”cen” fascorefxn=”dens_soft” strategy=”auto” fragbias=”density”

         rms=”%%rms%%” ncycles=”200″ fullatom=”0″ bbmove=”1″ nminsteps=”25″ temp=”4″ fraglens=”7″

         nfrags=”25″/>

      <CartesianSampler name=”cen5_60″ automode_scorecut=”-0.3″ scorefxn=”cen”

         mcscorefxn=”cen” fascorefxn=”dens_soft” strategy=”auto” fragbias=”density”

         rms=”%%rms%%” ncycles=”200″ fullatom=”0″ bbmove=”1″ nminsteps=”25″ temp=”4″ fraglens=”7″

         nfrags=”25″/>

      <CartesianSampler name=”cen5_70″ automode_scorecut=”-0.1″ scorefxn=”cen”

         mcscorefxn=”cen” fascorefxn=”dens_soft” strategy=”auto” fragbias=”density”

         rms=”%%rms%%” ncycles=”200″ fullatom=”0″ bbmove=”1″ nminsteps=”25″ temp=”4″ fraglens=”7″

         nfrags=”25″/>

      <CartesianSampler name=”cen5_80″ automode_scorecut=”0.0″ scorefxn=”cen”

         mcscorefxn=”cen” fascorefxn=”dens_soft” strategy=”auto” fragbias=”density”

         rms=”%%rms%%” ncycles=”200″ fullatom=”0″ bbmove=”1″ nminsteps=”25″ temp=”4″ fraglens=”7″

         nfrags=”25″/>

      <ReportFSC name=”report” testmap=”%%testmap%%” res_low=”10.0″ res_high=”%%reso%%”/>

      <BfactorFitting name=”fit_bs” max_iter=”50″ wt_adp=”0.0005″ init=”1″ exact=”1″/>

      <FastRelax name=”relaxcart” scorefxn=”dens” repeats=”1″ cartesian=”1″/>

   </MOVERS>

   <PROTOCOLS>

      <Add mover=”setupdens”/>

      <Add mover=”loaddens”/>

      <Add mover=”tocen”/>

      <Add mover=”cenmin”/>

      <Add mover=”relaxcart”/>

      <Add mover=”cen5_50″/>

      <Add mover=”relaxcart”/>

      <Add mover=”cen5_60″/>

      <Add mover=”relaxcart”/>

      <Add mover=”cen5_70″/>

      <Add mover=”relaxcart”/>

      <Add mover=”cen5_80″/>

      <Add mover=”relaxcart”/>

      <Add mover=”relaxcart”/>

      <Add mover=”report”/>

   </PROTOCOLS>

   <OUTPUT scorefxn=”dens”/>

</ROSETTASCRIPTS>

 

[Anonymous]

For the CartesianSampler, you would pass residues_to_exclude using the a residue selector.  For FastRelax, the easiest way to do it since you already will have a ResidueSelector, is through the MoveMapFactory: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/RosettaScripts#rosettascript-sections_move_map_factories

 

ResidueSelection docs: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/ResidueSelectors/ResidueSelectors

Very basic CartesianSampler docs: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/xsd/mover_CartesianSampler_type

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