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initial_HBNet_search.xml
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Searches for HBNets in heptads
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="beta" weights="beta_cst"/>
<ScoreFunction name="hard" weights="beta"/>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Index name="no_design_please" resnums="1-14,22-35,36-49,57-70,71-84,92-105,106-119,127-140"/>
<Index name="middle_heptad" resnums="15-21,50-56,85-91,120-126"/>
<Layer name="core_or_boundary" select_core="true" select_boundary="true" />
<Layer name="core" select_core="true" core_cutoff="4" /> =4?
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="no_design" selector="no_design_please">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<InitializeFromCommandline name="init"/>
ReadResfile name=resfile filename=resfile.txt />
<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" />
<LayerDesign name="init_layers" layer="Nterm_core_boundary_surface_Cterm" make_pymol_script="0" use_sidechain_neighbors="True" core="3.6" >
<core>
<Helix append="HNQYSTD"/>
</core>
<boundary>
<Helix exclude="EKRW"/>
</boundary>
</LayerDesign>
</TASKOPERATIONS>
<FILTERS>
<ScoreType name="scorefilter" scorefxn="hard" score_type="total_score" threshold="50.0" confidence="0" />
<EnzScore name="cst_score" score_type="cstE" scorefxn="beta" whole_pose="1" energy_cutoff="1" confidence="1"/>
<BuriedUnsatHbonds name="uhb" scorefxn="hard" cutoff="1" task_operations="init_layers,no_design" confidence="0"/>
<BuriedUnsatHbonds2 name="uhb2" scorefxn="hard" cutoff="1" task_operations="init_layers,no_design" AHD_cutoff="90" confidence="0"/>
<ResidueCount name="AA_count" max_residue_count="5" residue_types="ALA" residue_selector="middle_heptad" confidence="1"/>
<BuriedUnsatHbonds3 name="new_buns" scorefxn="hard" cutoff="20" print_out_info_to_pdb="true" use_hbnet_behavior="true" ignore_bb_heavy_unsats="false" confidence="1" residue_selector="middle_heptad"/>
</FILTERS>
<MOVERS>
<BundleGridSampler name="bgs1" scorefxn="hard" use_degrees="true" helix_length="35" reset="true" crick_params_file="alpha_helix_100" set_bondlengths="true" set_bondangles="true" set_dihedrals="true" > pre_selection_filter="scorefilter"
<Helix delta_omega0="0" invert="false" delta_omega1="%%delta_omega_1%%" r0="%%r_in_1%%" z1_offset="0" omega0="-2.85" />
<Helix delta_omega0="180" invert="false" delta_omega1="%%delta_omega_2%%" r0="%%r_in_2%%" z1_offset="%%z1_offset_1%%" pitch_from_helix="1" />
<Helix delta_omega0="90" invert="true" delta_omega1="%%delta_omega_3%%" r0="%%r_out_1%%" z1_offset="%%z1_offset_2%%" pitch_from_helix="1" />
<Helix delta_omega0="270" invert="true" delta_omega1="%%delta_omega_4%%" r0="%%r_out_2%%" z1_offset="%%z1_offset_3%%" pitch_from_helix="1" />
</BundleGridSampler>
<DeclareBond name="add_termini1" add_termini="true" atom1="C" atom2="N" res1="1" res2="2" />
#HBNet Mover definition
<HBNetStapleInterface scorefxn="beta" name="hbnet_interf" hb_threshold="-0.5" min_helices_contacted_by_network="4" core_selector="core" show_task="0" store_subnetworks="0" verbose="0" no_heavy_unsats_allowed="1" write_network_pdbs="0" min_network_size="4" max_unsat="0" min_core_res="3" min_unique_networks="1" write_cst_files="0" use_aa_dependent_weights="true" max_replicates_before_branch="3" min_connectivity="0.65" task_operations="arochi,init_layers,no_design" /> min_connectivity="0.65" ?
<MultiplePoseMover name="MPM_design" max_input_poses="50">
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="hard" weights="beta"/>
<ScoreFunction name="soft_cst" weights="/gscratch/baker/zibochen/scripts/weights/beta_soft_rep_cst.wts"/>
<ScoreFunction name="hard_cst" weights="beta_cst"/>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Index name="no_packing_please" resnums="1-7,29-35,36-42,64-70,71-77,99-105,106-112,134-140"/>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="no_packing" selector="no_packing_please">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<ConstrainHBondNetwork name="hbnet_task" />
<IncludeCurrent name="current"/>
<LimitAromaChi2 name="arochi" />
<ExtraRotamersGeneric name="ex1_ex2" ex1="1" ex2="1"/>
<ExtraRotamersGeneric name="ex1" ex1="1"/>
<LayerDesign name="layer_all" layer="core_boundary_surface_Nterm_Cterm" make_pymol_script="0" use_sidechain_neighbors="True" core="3.6" >
<core>
<Helix append="M" />
<Helix exclude="W" />
</core>
<boundary>
<Helix exclude="D" />
</boundary>
</LayerDesign>
</TASKOPERATIONS>
<MOVERS>
<PackRotamersMover name="softpack" scorefxn="soft_cst" task_operations="layer_all,no_packing,current,arochi,hbnet_task"/>
<PackRotamersMover name="hardpack" scorefxn="hard_cst" task_operations="layer_all,no_packing,current,arochi,ex1_ex2,hbnet_task"/>
<MinMover name="hardmin_sconly" scorefxn="hard_cst" chi="1" bb="0" bondangle="0" bondlength="0" />
</MOVERS>
<APPLY_TO_POSE>
</APPLY_TO_POSE>
<PROTOCOLS>
<Add mover="softpack"/>
<Add mover="hardmin_sconly"/>
<Add mover="hardpack"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
</MultiplePoseMover>
<MultiplePoseMover name="MPM_min_repack" max_input_poses="50">
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="hard" weights="beta" />
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Index name="no_packing_please" resnums="1-7,29-35,36-42,64-70,71-77,99-105,106-112,134-140"/>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="no_packing" selector="no_packing_please">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<RestrictToRepacking name="repack_only" />
<IncludeCurrent name="current"/>
<LimitAromaChi2 name="arochi" />
<ExtraRotamersGeneric name="ex1_ex2" ex1="1" ex2="1"/>
</TASKOPERATIONS>
<MOVERS>
<MinMover name="hardmin_sconly" scorefxn="hard" chi="1" bb="0" bondangle="0" bondlength="0" />
<PackRotamersMover name="repack" scorefxn="hard" task_operations="repack_only,ex1_ex2,current,arochi,no_packing" />
</MOVERS>
<APPLY_TO_POSE>
</APPLY_TO_POSE>
<PROTOCOLS>
<Add mover="hardmin_sconly" />
<Add mover="repack" />
</PROTOCOLS>
</ROSETTASCRIPTS>
</MultiplePoseMover>
<MultiplePoseMover name="MPM_filters" max_input_poses="50">
<SELECT>
<AndSelector>
<Filter filter="AA_count"/>
<Filter filter="cst_score"/>
<Filter filter="uhb"/>
<Filter filter="uhb2"/>
<Filter filter="new_buns"/>
</AndSelector>
</SELECT>
</MultiplePoseMover>
</MOVERS>
<PROTOCOLS>
<Add mover="bgs1"/>
<Add mover="add_termini1" />
<Add mover="hbnet_interf"/>
<Add mover_name="MPM_design"/>
<Add mover_name="MPM_min_repack"/>
<Add mover_name="MPM_filters"/>
</PROTOCOLS>
</ROSETTASCRIPTS>