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Stem_helix_backbone_grafting_script.txt
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Stem_helix_backbone_grafting_script.txt
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<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="sfxn_ref2015" weights="ref2015" />
</SCOREFXNS>
<TASKOPERATIONS>
<ProteinInterfaceDesign name="pido_far" interface_distance_cutoff="15"/>
<ProteinInterfaceDesign name="pido_med" interface_distance_cutoff="12"/>
<ProteinInterfaceDesign name="pido_near" interface_distance_cutoff="8"/>
<OperateOnCertainResidues name="hotspot_repack">
<ResiduePDBInfoHasLabel property="HOTSPOT"/>
<RestrictToRepackingRLT/>
</OperateOnCertainResidues>
<SelectBySASA name="core" mode="sc" state="bound" probe_radius="2.2" core_asa="0" surface_asa="30" core="1" boundary="0" surface="0"/>
<SelectBySASA name="core_and_boundary" mode="sc" state="bound" probe_radius="2.2" core_asa="0" surface_asa="30" core="1" boundary="1" surface="0"/>
</TASKOPERATIONS>
<FILTERS>
<ShapeComplementarity name="Sc" confidence="0" />
<Ddg name="ddg" scorefxn="sfxn_ref2015" confidence="0" />
<BuriedUnsatHbonds name="unsat" scorefxn="sfxn_ref2015" confidence="0"/>
<ScoreType name="farep" score_type="fa_rep" threshold="1000" confidence="0" />
<!--<Sasa name="sasa" threshold="700" hydrophobic="0" polar="0" jump="1" confidence="0" />
<ScoreType name="total_score" scorefxn="sfxn_ref2015" score_type="total_score" threshold="0" confidence="1"/>-->
</FILTERS>
<MOVERS>
<MinMover name="PreMinStructure" scorefxn="sfxn_ref2015" bb="true" chi="true" type="dfpmin" />
<MotifGraft name="motif_grafting"
context_structure="CC40.8_Ab.pdb" motif_structure="CC40.8_epitope.pdb"
RMSD_tolerance="5.0" NC_points_RMSD_tolerance="0.75"
clash_score_cutoff="5" clash_test_residue="ALA"
hotspots="2:5:6:8:9:10:12:13" combinatory_fragment_size_delta="1:1" max_fragment_replacement_size_delta="-4:4"
full_motif_bb_alignment="0" allow_independent_alignment_per_fragment="0"
graft_only_hotspots_by_replacement="0" only_allow_if_N_point_match_aa_identity="0"
only_allow_if_C_point_match_aa_identity="0" revert_graft_to_native_sequence="0" allow_repeat_same_graft_output="0" />
<build_Ala_pose name="ala_pose" partner1="0" partner2="1" interface_cutoff_distance="8" task_operations="hotspot_repack"/>
<Prepack name="ppk" jump_number="0"/>
<PackRotamersMover name="design_core" task_operations="hotspot_repack,pido_far,core"/>
<PackRotamersMover name="design_boundary" task_operations="hotspot_repack,pido_med,core_and_boundary"/>
<PackRotamersMover name="design_interface" task_operations="hotspot_repack,pido_near"/>
<MinMover name="sc_min" bb="0" chi="1" jump="0" />
<Backrub name="bckrub"/>
</MOVERS>
<APPLY_TO_POSE>
</APPLY_TO_POSE>
<PROTOCOLS >
<Add mover_name="PreMinStructure" />
<Add mover_name="motif_grafting" />
<Add mover_name="ala_pose" />
<Add mover_name="ppk" />
<Add mover_name="design_core" />
<Add mover_name="design_boundary" />
<Add mover_name="design_interface" />
<Add mover_name="bckrub" />
<Add mover_name="sc_min" />
<Add filter_name="unsat" />
<Add filter_name="ddg" />
<Add filter_name="Sc" />
<Add filter_name="farep" />
</PROTOCOLS>
</ROSETTASCRIPTS>