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redesign_c_terminal_helix_parallel.xml
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redesign_c_terminal_helix_parallel.xml
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<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="hard" weights="beta"/>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Chain name="peptide" chains="B"/>
<Chain name="SB76_trunc" chains="A"/>
<And name="scaffold_interface">
<InterfaceByVector>
<Chain chains="A"/>
<Chain chains="B"/>
</InterfaceByVector>
<Chain chains="A"/>
</And>
<And name="main_scaffold">
<Not selector="scaffold_interface"/>
<Chain chains="A"/>
</And>
<And name="peptide_interface">
<InterfaceByVector>
<Chain chains="A"/>
<Chain chains="B"/>
</InterfaceByVector>
<Chain chains="B"/>
</And>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="repack_new" selector="main_scaffold">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
</TASKOPERATIONS>
<MOVERS>
<SwitchChainOrder name="rechain" chain_order="12"/>
<HBNetStapleInterface scorefxn="hard" name="hbnet" start_selector="peptide_interface" design_residues="HYNQST" task_operations="repack_new" hb_threshold="-0.5" minimize="true" show_task="true" verbose="false" min_connectivity="0.6" min_helices_contacted_by_network="3" min_networks_per_pose="2" max_networks_per_pose="3" min_network_size="3" min_core_res="2" max_unsat="3" max_replicates_before_branch="3" use_aa_dependent_weights="true" write_network_pdbs="false" write_cst_files="false"/>
<BundleGridSampler name="bgs" use_degrees="true" helix_length="56" scorefxn="hard" crick_params_file="alpha_helix_100" set_bondlengths="true" set_bondangles="true" set_dihedrals="true" dump_pdbs="false" reset="false" max_samples="1000000000" nstruct_mode="true">
<Helix invert="true" delta_omega0="-60" delta_omega1_min="0" delta_omega1_max="340" delta_omega1_samples="18" r0_min="12.5" r0_max="13.5" r0_samples="3" z1_offset_min="0" z1_offset_max=".75" z1_offset_samples="2" delta_t="-22"/>
</BundleGridSampler>
<MultiplePoseMover name="switch_peptide_design_MPM" max_input_poses="100">
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="hard" weights="beta"/>
<ScoreFunction name="hard_cart" weights="beta_cart"/>
<ScoreFunction name="soft_cst" weights="/gscratch/baker/rlangan/weights/beta_soft_rep_cst.wts"/>
<ScoreFunction name="hard_cst" weights="beta_cst"/>
<ScoreFunction name="up_ele" weights="beta" >
<Reweight scoretype="fa_elec" weight="1.4" />
<Reweight scoretype="hbond_sc" weight="2.0" />
</ScoreFunction>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Layer name="hbnet_core" select_core="true" core_cutoff="3.6" />
<And name="terminal_loop">
<SecondaryStructure ss="L" include_terminal_loops="true" use_dssp="true"/>
<Index resnums="1-15"/>
<Chain chains="A"/>
</And>
<Layer name="pick_core_and_boundary" select_core="true" select_boundary="true" core_cutoff="5.2"/>
<Layer name="pick_core_and_surface" select_core="true" select_surface="true" core_cutoff="5.2"/>
<Layer name="pick_surface_and_boundary" select_surface="true" select_boundary="true" core_cutoff="5.2"/>
<Chain name="chain_a" chains="A"/>
<Layer name="core" select_core="true" core_cutoff="5.2" />
<ResidueName name="ala_and_met" residue_name3="ALA,MET" />
<Not name="not_ala_or_met" selector="ala_and_met" />
<!-- <ResiduePDBInfoHasLabel name="hbnet_residues" property="HBNet" /> -->
<And name="scaffold_interface">
<InterfaceByVector>
<Chain chains="A"/>
<Chain chains="B"/>
</InterfaceByVector>
<Chain chains="A"/>
</And>
<Index name="design_away" resnums="9,27,45,254,272,290"/>
<And name="main_scaffold">
<Not selector="scaffold_interface"/>
<Chain chains="A"/>
<Not selector="design_away"/>
</And>
<SecondaryStructure name="loops" ss="L"/>
<Neighborhood name="neighbors" selector="loops" distance="6"/>
<Not name="not_redesign">
<And>
<ResidueName residue_names="VAL"/>
<Chain chains="B"/>
</And>
</Not>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<ConsensusLoopDesign name="disallow_non_abego_aas"/>
<LayerDesign name="layer_all" layer="core_boundary_surface_Nterm_Cterm" make_pymol_script="0" use_sidechain_neighbors="True" core="4.2" >
<core>
Helix append="M" />
<Helix exclude="WY" />
</core>
<boundary>
<Helix exclude="WMY" />
</boundary>
<surface>
<Helix append="A"/>
</surface>
</LayerDesign>
<OperateOnResidueSubset name="loop_design" selector="not_redesign">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="repack_new" selector="main_scaffold">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="design_core" selector="pick_surface_and_boundary">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="design_boundary" selector="pick_core_and_surface">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="design_surface" selector="pick_core_and_boundary">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="repack_not_ala_or_met" selector="not_ala_or_met" >
<RestrictToRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="redesign_ala_met" selector="ala_and_met" >
<RestrictAbsentCanonicalAASRLT aas="AMILVF" />
</OperateOnResidueSubset>
<InitializeFromCommandline name="init"/>
<ConstrainHBondNetwork name="hbnet_task" />
<IncludeCurrent name="current"/>
<LimitAromaChi2 name="arochi" />
<ExtraRotamersGeneric name="ex1_ex2" ex1="1" ex2="1"/>
<ExtraRotamersGeneric name="ex1" ex1="1"/>
<RestrictAbsentCanonicalAAS name="ala_only" resnum="0" keep_aas="A" />
<RestrictToRepacking name="repack_only"/>
BundleReporter name=bundle_filter scorefxn=hard/>
</TASKOPERATIONS>
<MOVERS>
<PackRotamersMover name="softpack_core" scorefxn="soft_cst" task_operations="layer_all,design_core,current,arochi,disallow_non_abego_aas,repack_new,hbnet_task"/>
<PackRotamersMover name="softpack_boundary" scorefxn="soft_cst" task_operations="layer_all,design_boundary,current,arochi,disallow_non_abego_aas,repack_new,hbnet_task"/>
<PackRotamersMover name="softpack_surface" scorefxn="soft_cst" task_operations="layer_all,design_surface,current,arochi,disallow_non_abego_aas,repack_new,hbnet_task"/>
<PackRotamersMover name="hardpack_core" scorefxn="hard_cst" task_operations="layer_all,design_core,current,arochi,ex1_ex2,disallow_non_abego_aas,repack_new,hbnet_task"/>
<PackRotamersMover name="hardpack_boundary" scorefxn="hard_cst" task_operations="layer_all,design_boundary,current,arochi,ex1_ex2,disallow_non_abego_aas,repack_new,hbnet_task"/>
<PackRotamersMover name="hardpack_surface" scorefxn="up_ele" task_operations="layer_all,design_surface,current,arochi,ex1,disallow_non_abego_aas,repack_new,hbnet_task"/>
<PackRotamersMover name="design_loops" scorefxn="hard_cst" task_operations="current,arochi,ex1_ex2,loop_design,layer_all,disallow_non_abego_aas,hbnet_task"/>
<DumpPdb name="dump1" fname="dump1.pdb" scorefxn="hard"/>
ConnectChainsMover name=closer chain_connections="[A+B],[B+A]"/>
InterfaceAnalyzerMover name=interface_analyzer scorefxn=hard packstat=1 pack_separated=0 />
<MinMover name="hardmin_sconly" scorefxn="hard_cst" chi="1" bb="0" bondangle="0" bondlength="0" />
</MOVERS>
<PROTOCOLS>
<Add mover="softpack_core"/>
<Add mover="softpack_boundary"/>
<Add mover="softpack_surface"/>
<Add mover="hardmin_sconly"/>
<Add mover="hardpack_core"/>
<Add mover="hardpack_boundary"/>
<Add mover="hardpack_surface"/>
Add mover=interface_analyzer/>
Add mover=dump1/>
Add mover=closer/>
Add mover=design_loops/>
</PROTOCOLS>
</ROSETTASCRIPTS>
</MultiplePoseMover>
<MultiplePoseMover name="MPM_filters">
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="hard_cst" weights="beta_cst"/>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Chain name="peptide" chains="B"/>
<Chain name="SB76_trunc" chains="A"/>
<InterfaceByVector name="scaffold_interface">
<Chain chains="A"/>
<Not selector="SB76_trunc"/>
</InterfaceByVector>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<LayerDesign name="layer_all" layer="core_boundary_surface_Nterm_Cterm" make_pymol_script="0" use_sidechain_neighbors="True" core="5.2" >
<core>
Helix append="M" />
<Helix exclude="WY" />
</core>
<boundary>
<Helix exclude="DWMY" />
</boundary>
<surface>
<Helix append="A"/>
</surface>
</LayerDesign>
</TASKOPERATIONS>
<FILTERS>
<PreProline name="prepro" use_statistical_potential="0" />
<ScoreType name="scorefilter" scorefxn="hard_cst" score_type="total_score" threshold="0.0" confidence="1" />
<EnzScore name="cst_score" score_type="cstE" scorefxn="hard_cst" whole_pose="1" energy_cutoff="5" confidence="1"/>
<BuriedUnsatHbonds3 name="buns3" scorefxn="beta" cutoff="20" print_out_info_to_pdb="true" use_hbnet_behavior="true" confidence="0" ignore_bb_heavy_unsats="true"/>
<ResidueCount name="ala_count" max_residue_count="15" residue_types="ALA" residue_selector="scaffold_interface" confidence="1"/>
</FILTERS>
<PROTOCOLS>
Add filter=prepro/>
<Add filter="scorefilter"/>
<Add filter="cst_score"/>
<Add filter="ala_count"/>
<Add filter="buns3"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
</MultiplePoseMover>
<MultiplePoseMover name="analyze">
<ROSETTASCRIPTS>
<SCOREFXNS>
### add Nov15 energy function with coordinate constraints
<ScoreFunction name="NOV15" weights="beta" />
</SCOREFXNS>
<TASKOPERATIONS>
</TASKOPERATIONS>
<RESIDUE_SELECTORS>
</RESIDUE_SELECTORS>
<FILTERS>
</FILTERS>
<MOVERS>
<InterfaceAnalyzerMover name="interface_analyzer" scorefxn="NOV15" packstat="true" interface_sc="true" pack_input="false" pack_separated="true" fixedchains="B" tracer="true" />
</MOVERS>
<PROTOCOLS>
<Add mover_name="interface_analyzer" />
</PROTOCOLS>
</ROSETTASCRIPTS>
</MultiplePoseMover>
</MOVERS>
<PROTOCOLS>
<Add mover="bgs"/>
<Add mover="rechain"/>
<Add mover="hbnet"/>
Add mover=relax_new_interface/>
<Add mover="switch_peptide_design_MPM"/>
<Add mover="MPM_filters"/>
Add mover=analyze/>
</PROTOCOLS>
</ROSETTASCRIPTS>