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AbPredict_xsd.xml
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AbPredict_xsd.xml
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<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="PSSMscorefxn">
<Reweight scoretype="res_type_constraint" weight="0.2"/>
</ScoreFunction>
<ScoreFunction name="soft_rep_res_type_cst" weights="soft_rep">
<Reweight scoretype="res_type_constraint" weight="0.2"/>
</ScoreFunction>
<ScoreFunction name="talaris_cal" weights="ref2015">
<Reweight scoretype="coordinate_constraint" weight="0.5"/>
<Reweight scoretype="dihedral_constraint" weight="1"/>
<Reweight scoretype="res_type_constraint" weight="0.5"/>
<Reweight scoretype="chainbreak" weight="10"/>
</ScoreFunction>
<ScoreFunction name="TalarisCal_coordcst" weights="ref2015">
<Reweight scoretype="res_type_constraint" weight="0.3"/>
</ScoreFunction>
<ScoreFunction name="soft_rep_coordcst" weights="soft_rep">
<Reweight scoretype="coordinate_constraint" weight="0.06"/>
</ScoreFunction>
<ScoreFunction name="ref15_seq_const" weights="ref2015">
<Reweight scoretype="res_type_constraint" weight="0.5"/>
</ScoreFunction>
<ScoreFunction name="sc12_atr_rep">
<Reweight scoretype="fa_atr" weight="0.8"/>
<Reweight scoretype="fa_rep" weight="0.44"/>
</ScoreFunction>
<ScoreFunction name="talaris_full" weights="ref2015">
<Reweight scoretype="coordinate_constraint" weight="5"/>
</ScoreFunction>
<ScoreFunction name="soft_rep_full" weights="soft_rep">
<Reweight scoretype="coordinate_constraint" weight="5"/>
</ScoreFunction>
<ScoreFunction name="tal_no_pssm" weights="ref2015">
<Reweight scoretype="coordinate_constraint" weight="5"/>
</ScoreFunction>
<ScoreFunction name="talaris_pure" weights="ref2015"/>
<ScoreFunction name="light_coor_const" weights="ref2015">
<Reweight scoretype="coordinate_constraint" weight="0.1"/>
</ScoreFunction>
<ScoreFunction name="light_coor_const_soft" weights="soft_rep">
<Reweight scoretype="coordinate_constraint" weight="0.1"/>
</ScoreFunction>
</SCOREFXNS>
<TASKOPERATIONS>
<ThreadSequence name="thread_original" allow_design_around="0" target_sequence="%%sequence%%"/>
<InitializeFromCommandline name="init"/>
<NoRepackDisulfides name="noRepackDisulfs"/>
<RestrictToRepacking name="rtr"/>
</TASKOPERATIONS>
#-----------------------------------------------------------------
# General BB-Clash checker
#-----------------------------------------------------------------
<TASKOPERATIONS>
<ProteinInterfaceDesign name="design_chain1_only" design_chain1="1" design_chain2="0" repack_chain1="1" repack_chain2="0" modify_before_jump="1" modify_after_jump="0" interface_distance_cutoff="100"/>
<RestrictAbsentCanonicalAAS name="design_only_Ala" keep_aas="A"/>
<ProteinInterfaceDesign name="repack_chain2_only" design_chain1="0" design_chain2="0" repack_chain1="0" repack_chain2="1" interface_distance_cutoff="10" modify_after_jump="1" modify_before_jump="0"/>
</TASKOPERATIONS>
<MOVERS>
<PackRotamersMover name="quick_repack" scorefxn="soft_rep_coordcst" task_operations="init,thread_original"/>
</MOVERS>
<FILTERS>
<ScoreType name="total_score" score_type="total_score" scorefxn="TalarisCal_coordcst" threshold="1000000"/>
ScoreType name="clash_score" score_type="total_score" scorefxn="soft_rep_coordcst" threshold="100000" confidence="0"/>
MoveBeforeFilter name="bb_clash_check" mover="design_softrep" filter="clash_score"/>
<Time name="refine_time"/>
<Time name="build_time"/>
</FILTERS>
<MOVERS> build starting structure
<SpliceInAntibody name="H1_H2_build" torsion_database="%%H1_H2.db%%" scorefxn="talaris_cal" repack_shell="0.1" design_shell="0.1" template_file="%%template_pdb%%" task_operations="init,rtr,noRepackDisulfs" debug="0" min_seg="1" delta_lengths="0" database_pdb_entry="%%entry_H1_H2%%" segment="H1_H2" use_sequence_profile="0"/>
<SpliceInAntibody name="H3_build" torsion_database="%%H3.db%%" scorefxn="talaris_cal" repack_shell="0.1" design_shell="0.1" template_file="%%template_pdb%%" task_operations="init,rtr,noRepackDisulfs" debug="0" min_seg="1" delta_lengths="0" database_pdb_entry="%%entry_H3%%" segment="H3" use_sequence_profile="0"/>
<SpliceInAntibody name="L1_L2_build" torsion_database="%%L1_L2.db%%" scorefxn="talaris_cal" repack_shell="0.1" design_shell="0.1" template_file="%%template_pdb%%" task_operations="init,rtr,noRepackDisulfs" debug="0" min_seg="1" delta_lengths="0" database_pdb_entry="%%entry_L1_L2%%" segment="L1_L2" use_sequence_profile="0"/>
<SpliceInAntibody name="L3_build" torsion_database="%%L3.db%%" scorefxn="talaris_cal" repack_shell="0.1" design_shell="0.1" template_file="%%template_pdb%%" task_operations="init,rtr,noRepackDisulfs" debug="0" min_seg="1" delta_lengths="0" database_pdb_entry="%%entry_L3%%" segment="L3" use_sequence_profile="0"/>
</MOVERS>
<MOVERS> refinement
<DumpPdb name="After_rb" fname="After_rb.pdb"/>
After_rb
<SpliceInAntibody name="H1_H2" torsion_database="%%H1_H2.db%%" scorefxn="talaris_cal" repack_shell="6" design_shell="6" template_file="%%template_pdb%%" task_operations="init,noRepackDisulfs,thread_original" debug="0" min_seg="1" delta_lengths="0" dbase_iterate="1" segment="H1_H2" use_sequence_profile="0"/>
<SpliceInAntibody name="H3" torsion_database="%%H3.db%%" scorefxn="talaris_cal" repack_shell="6" design_shell="6" template_file="%%template_pdb%%" task_operations="init,thread_original,noRepackDisulfs" debug="0" min_seg="1" delta_lengths="0" dbase_iterate="1" segment="H3" use_sequence_profile="0"/>
<SpliceInAntibody name="L1_L2" torsion_database="%%L1_L2.db%%" scorefxn="talaris_cal" repack_shell="6" design_shell="6" template_file="%%template_pdb%%" task_operations="init,thread_original,noRepackDisulfs" debug="0" min_seg="1" delta_lengths="0" dbase_iterate="1" segment="L1_L2" use_sequence_profile="0"/>
<SpliceInAntibody name="L3" torsion_database="%%L3.db%%" scorefxn="talaris_cal" repack_shell="6" design_shell="6" template_file="%%template_pdb%%" task_operations="init,thread_original,noRepackDisulfs" debug="0" min_seg="1" delta_lengths="0" dbase_iterate="1" segment="L3" use_sequence_profile="0"/>
<PackRotamersMover name="soft_design" scorefxn="soft_rep_full" task_operations="thread_original,init,noRepackDisulfs"/>
<PackRotamersMover name="hard_design" scorefxn="talaris_full" task_operations="init,rtr,noRepackDisulfs"/>
<RotamerTrialsMinMover name="RTmin" scorefxn="talaris_full" task_operations="init,rtr,noRepackDisulfs"/>
<TaskAwareMinMover name="soft_min" scorefxn="soft_rep_full" chi="1" bb="0" jump="0" task_operations="init,noRepackDisulfs"/>
<TaskAwareMinMover name="soft_min_all" scorefxn="light_coor_const_soft" chi="1" bb="1" jump="1" task_operations="init,noRepackDisulfs"/>
<TaskAwareMinMover name="hard_min" scorefxn="talaris_full" chi="1" bb="0" jump="1" task_operations="init,noRepackDisulfs"/>
<TaskAwareMinMover name="hard_min_all" scorefxn="light_coor_const" chi="1" bb="1" jump="1" task_operations="init,noRepackDisulfs"/>
<AddConstraintsToCurrentConformationMover name="addCAconst" />
<ClearConstraintsMover name="clc" />
<AtomTree name="docking_ft" docking_ft="1"/>
<AtomTree name="two_parts_chain1" two_parts_chain1="1"/>
<AtomTree name="AB_atom_tree" ab_fold_tree="1"/>
<AtomTree name="simple_ft" simple_ft="1"/>
<PackRotamersMover name="thread_ori_sequence" scorefxn="soft_rep_coordcst" task_operations="init,thread_original,noRepackDisulfs"/>
<ParsedProtocol name="post_splice_refine">
<Add mover_name="addCAconst"/>
<Add mover="AB_atom_tree"/>
<Add mover_name="soft_design"/>
<Add mover_name="soft_min"/>
<Add mover_name="soft_design"/>
<Add mover_name="hard_min"/>
<Add mover_name="hard_design"/>
<Add mover_name="hard_min"/>
<Add mover_name="hard_design"/>
Add mover_name="RTmin"/>
Add mover_name="RTmin"/>
Add mover_name="RTmin"/>
<Add mover_name="hard_min"/>
<Add mover_name="simple_ft"/>
<Add mover_name="clc"/>
</ParsedProtocol>
<ParsedProtocol name="splice_refine_L1_L2">
<Add mover="L1_L2"/>
<Add mover="post_splice_refine"/>
</ParsedProtocol>
<ParsedProtocol name="splice_refine_L3">
<Add mover="L3"/>
<Add mover="post_splice_refine"/>
</ParsedProtocol>
<ParsedProtocol name="splice_refine_H1_H2">
<Add mover="H1_H2"/>
<Add mover="post_splice_refine"/>
</ParsedProtocol>
<ParsedProtocol name="splice_refine_H3">
<Add mover="H3"/>
<Add mover="post_splice_refine"/>
</ParsedProtocol>
<LoadPDB name="load_from_checkpoint" filename="%%prefix%%.checkpoint.pdb"/>
</MOVERS>
<FILTERS> checkpointing stuff
<FileExist name="recover" filename="%%prefix%%.checkpoint.pdb" ignore_zero_byte="1"/>
<FileRemove name="remove_checkpointing_files" delete_content_only="1" filenames="%%prefix%%.stability.checkpoint,%%prefix%%.ddg.checkpoint,%%prefix%%.checkpoint.pdb,%%prefix%%.mc1.checkpoint,%%prefix%%.mc2.checkpoint,%%prefix%%.mc3.checkpoint,%%prefix%%.mc4.checkpoint"/>
<PoseInfo name="getPoseInfoBeforeSwap"/>
</FILTERS>
<MOVERS>
<If name="if_checkpoint_load" filter_name="recover" true_mover_name="load_from_checkpoint"/>
<ClearConstraintsMover name="clear_constraints"/>
<RBIn name="rb_transform" rigid_body_dbase="%%rb.db%%" from_entry="1" to_entry="1340" randomize="true"/>
<PackRotamersMover name="design_softrep_rb" scorefxn="soft_rep_coordcst" task_operations="init,thread_original,noRepackDisulfs"/>
<PackRotamersMover name="design_talarisCal_rb" scorefxn="TalarisCal_coordcst" task_operations="init,thread_original,noRepackDisulfs"/>
<RotamerTrialsMinMover name="rtmin_rb" task_operations="init,thread_original,noRepackDisulfs" scorefxn="TalarisCal_coordcst"/>
<ParsedProtocol name="RBMove">
Add mover=dumpme9/>
<Add mover="clear_constraints"/>
<Add mover="addCAconst"/>
<Add mover="rb_transform"/>
Add mover="After_rb"/>
<Add mover="AB_atom_tree"/>
<Add mover="design_softrep_rb"/>
<Add mover="soft_min"/>
<Add mover="hard_min"/>
<Add mover="design_talarisCal_rb"/>
Add mover="rtmin_rb"/>
<Add mover="hard_min"/>
<Add mover_name="simple_ft"/>
<Add mover="clear_constraints"/>
</ParsedProtocol>
<ParsedProtocol name="splice_rbmin_menu" mode="single_random"> Probabilities for optimal splice/rbmove guestimated by norn/sarel.
<Add mover="splice_refine_H3" apply_probability="0.40"/> est. accept p = 0.13
<Add mover="splice_refine_L3" apply_probability="0.1"/> est. accept p = 0.27
<Add mover="splice_refine_L1_L2" apply_probability="0.1"/> est. accept p = 0.28
<Add mover="splice_refine_H1_H2" apply_probability="0.15"/> 0.25/> 0.25 est. accept p = 0.20
<Add mover="RBMove" apply_probability="0.25"/> est. accept p = 0.42
</ParsedProtocol>
Splice name="splice_seqconstraints" protein_family="antibodies" segment="L3" scorefxn="TalarisCal_coordcst" add_sequence_constraints_only="1"/>
<GenericSimulatedAnnealer name="annealer" mover_name="splice_rbmin_menu" filter_name="total_score" trials="50" preapply="0" /> Instead of using Chris's multiple MC moves I am doing one 150 step SA-MC
<ParsedProtocol name="post_run_refine">
<Add mover_name="addCAconst"/>
<Add mover="AB_atom_tree"/>
<Add mover_name="soft_design"/>
<Add mover_name="soft_min_all"/>
<Add mover_name="soft_design"/>
<Add mover_name="hard_min_all"/>
<Add mover_name="hard_design"/>
<Add mover_name="hard_min_all"/>
<Add mover_name="hard_design"/>
<Add mover_name="hard_design"/>
<Add mover_name="RTmin"/>
<Add mover_name="RTmin"/>
<Add mover_name="RTmin"/>
<Add mover_name="hard_min_all"/>
<Add mover_name="simple_ft"/>
<Add mover_name="clc"/>
</ParsedProtocol>
</MOVERS>
<PROTOCOLS>
<Add filter="build_time"/>
<Add mover="H1_H2_build"/>
<Add mover="L1_L2_build"/>
<Add mover="L3_build"/>
<Add mover="H3_build"/>
<Add mover="RBMove"/>
<Add mover="thread_ori_sequence"/>
Add filter="build_time"/>
<Add mover="post_splice_refine"/>
Add mover="splice_refine_H1_H2"/>
<Add mover="annealer"/>
<Add mover="post_run_refine"/>
</PROTOCOLS>
<OUTPUT scorefxn="TalarisCal_coordcst"/>
</ROSETTASCRIPTS>