OneScience-Group/flex_ddG_tutorial

1<ROSETTASCRIPTS>2  <SCOREFXNS>3    <ScoreFunction name="fa_fxn" weights="talaris2014"/>4    <ScoreFunction name="fa_fxn_cst" weights="talaris2014">5      <Reweight scoretype="atom_pair_constraint" weight="1.0"/>6      <Set fa_max_dis="9.0"/>7    </ScoreFunction>8  </SCOREFXNS>9 10  <TASKOPERATIONS>11    <ReadResfile name="res_mutate" filename="%%mutate_resfile_relpath%%"/>12  </TASKOPERATIONS>13 14  <RESIDUE_SELECTORS>15    <Task name="resselector" fixed="0" packable="0" designable="1" task_operations="res_mutate"/>16    <Neighborhood name="bubble_helper" selector="resselector" distance="%%neighbor_distance%%" include_focus_in_subset="true"/>17    <NativeSelector name="bubble" residue_selector="bubble_helper" />18    <PrimarySequenceNeighborhood name="bubble_adjacent" selector="bubble" lower="1" upper="1"/>19    <StoredResidueSubset name="restore_neighbor_shell" subset_name="neighbor_shell"/>20    <Not name="everythingelse" selector="restore_neighbor_shell"/>21  </RESIDUE_SELECTORS>22  <TASKOPERATIONS>23    <OperateOnResidueSubset name="repackonly" selector="restore_neighbor_shell">24      <RestrictToRepackingRLT/>25    </OperateOnResidueSubset>26    <OperateOnResidueSubset name="norepack" selector="everythingelse">27      <PreventRepackingRLT/>28    </OperateOnResidueSubset>29    <UseMultiCoolAnnealer name="multicool" states="6"/>30    <ExtraChiCutoff name="extrachizero" extrachi_cutoff="0"/>31    <InitializeFromCommandline name="commandline_init"/>32    <RestrictToRepacking name="restrict_to_repacking"/>33  </TASKOPERATIONS>34 35  <MOVERS>36    <AddConstraintsToCurrentConformationMover name="addcst" use_distance_cst="1" coord_dev="0.5" min_seq_sep="0" max_distance="9" CA_only="1" bound_width="0.0" cst_weight="0.0"/>37    <ClearConstraintsMover name="clearcst"/>38    <MinMover name="minimize" scorefxn="fa_fxn_cst" chi="1" bb="1" type="lbfgs_armijo_nonmonotone" tolerance="%%min_tolerance%%" max_iter="%%min_max_iter%%" abs_score_convergence_threshold="%%min_abs_score_convergence_threshold%%"/>39 40    <PackRotamersMover name="mutate" scorefxn="fa_fxn" task_operations="commandline_init,res_mutate,norepack,multicool"/>41 42    <ReportToDB name="dbreport" batch_description="interface_ddG" database_name="ddG.db3">43      <ResidueFeatures/>44      <ScoreTypeFeatures/>45      <ScoreFunctionFeatures scorefxn="fa_fxn"/>46      <StructureScoresFeatures scorefxn="fa_fxn"/>47      <HBondFeatures scorefxn="fa_fxn"/>48      <InterfaceFeatures scorefxn="fa_fxn" pack_together="false"/>49    </ReportToDB>50 51    <ReportToDB name="structreport" batch_description="interface_ddG_struct" database_name="struct.db3">52      <PoseConformationFeatures/>53      <PdbDataFeatures/>54      <JobDataFeatures/>55      <ResidueFeatures/>56      <PoseCommentsFeatures/>57      <ProteinResidueConformationFeatures/>58      <ResidueConformationFeatures/>59      <RotamerFeatures/>60      <ResidueBurialFeatures/>61    </ReportToDB>62 63    <SavePoseMover name="save_wt_bound_pose" restore_pose="0" reference_name="wt_bound_pose"/>64    <LoadPDB name="load_backrub_pdb" filename="%%backrub_pdb_path%%"/>65 66    <InterfaceDdGMover name="int_ddG_mover" wt_ref_savepose_mover="save_wt_bound_pose" chain_name="%%chainstomove%%" db_reporter="dbreport" scorefxn="fa_fxn"/>67 68    <ScoreMover name="apply_score" scorefxn="fa_fxn_cst" verbose="0"/>69    <StoreResidueSubset name="neighbor_shell_storer" subset_name="neighbor_shell" residue_selector="bubble_adjacent" />70 71  </MOVERS>72  <APPLY_TO_POSE>73  </APPLY_TO_POSE>74  <PROTOCOLS>75    <Add mover_name="save_wt_bound_pose"/>76 77    <Add mover_name="load_backrub_pdb"/>78    <Add mover_name="neighbor_shell_storer"/>79 80    <Add mover_name="addcst"/>81    <Add mover_name="apply_score"/>82    <Add mover_name="clearcst"/>83    <Add mover_name="mutate"/>84 85    <Add mover_name="addcst"/>86    <Add mover_name="minimize"/>87    <Add mover_name="clearcst"/>88    <Add mover_name="structreport"/>89 90    <Add mover_name="int_ddG_mover"/>91 92    <Add mover_name="dbreport"/>93  </PROTOCOLS>94  <OUTPUT />95</ROSETTASCRIPTS>96