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Fixing certain residues during refinement

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Fixing certain residues during refinement
#1

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>

 

Category: 
Post Situation: 
Thu, 2019-08-29 14:00
ckdenist

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

Thu, 2019-08-29 14:29
jadolfbr