Autogenerated Tag Syntax Documentation:
Builds an assembly around the segment provided in the input PDB file
<AppendAssemblyMover name="(&string;)" start_temperature="(0.6 ℜ)"
end_temperature="(0.6 ℜ)" add_probability="(0.05 ℜ)"
delete_probability="(0.005 ℜ)"
conformer_switch_probability="(0 ℜ)"
window_width="(4 &positive_integer;)"
minimum_cycles="(10000 &non_negative_integer;)"
maximum_cycles="(100000 &non_negative_integer;)"
model_file_name="(&string;)" hashed="(false &bool;)"
edge_file_name="(&string;)" max_segments="(100 &non_negative_integer;)"
max_segment_length="(100 &non_negative_integer;)"
output_pose_per_move="(false &bool;)"
recover_lowest_assembly="(true &bool;)"
recursive_depth="(1 &non_negative_integer;)"
pose_segment_starts="(&int_cslist;)" pose_segment_ends="(&int_cslist;)"
pose_segment_dssp="(&string;)" strict_dssp_changes="(false &bool;)"
set_segments_from_dssp="(false &bool;)" match_segments="(&int_cslist;)"
partner_pdb="(&string;)"
required_resnums="(&refpose_enabled_residue_number_cslist;)"
max_recursion="(1 &non_negative_integer;)"
modifiable_terminus="(B &string;)" output_partner="(true &bool;)"
extend_mode="(false &bool;)" start_node_vital_segments="(all &string;)"
required_selector="(&string;)" >
<AssemblyScorers >
<InterModelMotifScorer name="(&string;)" weight="(1.0 ℜ)" />
<IntraDesignTerminusMotifScorer name="(&string;)" weight="(1.0 ℜ)"
optimum_distance="(ℜ)" maximum_unpenalized_variance="(ℜ)" />
<LigandScorer name="(&string;)" weight="(1.0 ℜ)"
ligand_interaction_cutoff_distance="(5.0 ℜ)" />
<MotifScorer name="(&string;)" weight="(1.0 ℜ)" />
<PartnerMotifScorer name="(&string;)" weight="(1.0 ℜ)" />
<SegmentContactOrderScorer name="(&string;)" weight="(1.0 ℜ)" />
<StartingNodeMotifScorer name="(&string;)" weight="(1.0 ℜ)" />
<SubsetPartnerMotifScorer name="(&string;)" weight="(1.0 ℜ)"
region_start="(1 &non_negative_integer;)"
region_end="(2 &non_negative_integer;)" />
<TerminusMotifScorer name="(&string;)" weight="(1.0 ℜ)"
partner_residue="(&non_negative_integer;)" optimum_distance="(ℜ)"
maximum_unpenalized_variance="(ℜ)" terminus="(&string;)" />
<TopNMotifScorer name="(&string;)" weight="(1.0 ℜ)"
scores_to_keep="(1 &non_negative_integer;)" />
</AssemblyScorers>
<AssemblyRequirements >
<ClashRequirement name="(&string;)"
maximum_clashes_allowed="(0 &non_negative_integer;)"
clash_radius="(4.0 ℜ)" />
<DsspSpecificLengthRequirement name="(&string;)" dssp_code="(X &dssp_enum;)"
maximum_length="(100 &non_negative_integer;)"
minimum_length="(0 &non_negative_integer;)" />
<KeepLigandContactsRequirement name="(&string;)"
contact_distance_cutoff="(2.5 ℜ)" />
<LengthInResiduesRequirement name="(&string;)"
maximum_length="(10000 &non_negative_integer;)"
minimum_length="(0 &non_negative_integer;)" />
<LigandClashRequirement name="(&string;)"
maximum_clashes_allowed="(0 &non_negative_integer;)"
clash_radius="(4.0 ℜ)" />
<NonTerminalStartingSegmentRequirement />
<SizeInSegmentsRequirement name="(&string;)"
maximum_size="(10000 &non_negative_integer;)"
minimum_size="(0 &non_negative_integer;)" />
</AssemblyRequirements>
<Ligands >
<Ligand partner_ligand="(false &bool;)" pdb_conformers="(&string;)"
alignment_atoms="(&string;)" auto_detect_contacts="(true &bool;)"
ligand_resnum="(&refpose_enabled_residue_number;)"
ligand_selector="(&string;)" >
<Contact partner_contact="(false &bool;)"
contact_resnum="(&refpose_enabled_residue_number;)"
ligand_atom_name="(&string;)" contact_atom_name="(&string;)" />
<Coordination coordination_files="(&string;)"
geometry_score_threshold="(1 ℜ)" >
<IdealContacts distance="(ℜ)" angle="(109.5 ℜ)"
dihedral_1="(30 ℜ)" dihedral_2="(30 ℜ)"
max_coordinating_atoms="(&non_negative_integer;)"
ligand_atom_name="(&string;)" />
</Coordination>
</Ligand>
</Ligands>
</AppendAssemblyMover>
Subtag AssemblyScorers: The subtags of this tag define the AssemblyScoreFunction that will be used to evaluate assemblies
Subtag InterModelMotifScorer: Basic Motif score among non-adjacent helices
Subtag IntraDesignTerminusMotifScorer: Motif score to measure packing of assembly against partner PDB
Subtag LigandScorer: Scores how well ligand is buried based on orientation of nearby Ca's
Subtag MotifScorer: Basic Motif score among all helices
Subtag PartnerMotifScorer: Motif score to measure packing of assembly against partner PDB
Subtag SegmentContactOrderScorer: Favors assemblies whose segments form contacts with segments distant in the assembly
Subtag StartingNodeMotifScorer: Specifically scores packing against the starting node
Subtag SubsetPartnerMotifScorer: Motif score to measure packing of assembly against partner PDB
Subtag TerminusMotifScorer: Motif score to measure packing of assembly against partner PDB
Subtag TopNMotifScorer: Basic Motif score among all helices
Subtag AssemblyRequirements: Subtags of this tag define the set of requirements that will be used when evaluating SEWING assemblies
Subtag ClashRequirement: Checks for clashes between segments in the assembly
Subtag DsspSpecificLengthRequirement: Restricts the number of residues in segments with the specified DSSP
Subtag KeepLigandContactsRequirement: Fails if an assembly's ligands lose more than a set number of contacts
Subtag LengthInResiduesRequirement: Checks the number of segments in the assembly
Subtag LigandClashRequirement: Checks for clashes between the assembly and its ligands
Subtag SizeInSegmentsRequirement: Checks the number of segments in the assembly
Subtag Ligands: Subtags of this tag specify the ligands present in the input pose and their respective protein contacts.
Subtag Ligand: Specifies the position of a ligand and the contacts that it forms with the input pose
Subtag Contact:
Subtag Coordination: Contains subtags defining ideal coordination environments for atoms in the ligand
Subtag IdealContacts: