scripting_documentation/RosettaScripts/xsd/mover_AssemblyMover

Autogenerated Tag Syntax Documentation:

Basic SEWING mover for generating assemblies using random substructures. Uses Monte Carlo sampling and scores based on motif score measuring potential packing interactions.

<AssemblyMover name="(&string;)" start_temperature="(0.6 &real;)"
        end_temperature="(0.6 &real;)" add_probability="(0.05 &real;)"
        delete_probability="(0.005 &real;)"
        conformer_switch_probability="(0 &real;)"
        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;)" >
    <AssemblyScorers >
        <InterModelMotifScorer name="(&string;)" weight="(1.0 &real;)" />
        <IntraDesignTerminusMotifScorer name="(&string;)" weight="(1.0 &real;)"
                optimum_distance="(&real;)" maximum_unpenalized_variance="(&real;)" />
        <LigandScorer name="(&string;)" weight="(1.0 &real;)"
                ligand_interaction_cutoff_distance="(5.0 &real;)" />
        <MotifScorer name="(&string;)" weight="(1.0 &real;)" />
        <PartnerMotifScorer name="(&string;)" weight="(1.0 &real;)" />
        <SegmentContactOrderScorer name="(&string;)" weight="(1.0 &real;)" />
        <StartingNodeMotifScorer name="(&string;)" weight="(1.0 &real;)" />
        <SubsetPartnerMotifScorer name="(&string;)" weight="(1.0 &real;)"
                region_start="(1 &non_negative_integer;)"
                region_end="(2 &non_negative_integer;)" />
        <TerminusMotifScorer name="(&string;)" weight="(1.0 &real;)"
                partner_residue="(&non_negative_integer;)" optimum_distance="(&real;)"
                maximum_unpenalized_variance="(&real;)" terminus="(&string;)" />
        <TopNMotifScorer name="(&string;)" weight="(1.0 &real;)"
                scores_to_keep="(1 &non_negative_integer;)" />
    </AssemblyScorers>
    <AssemblyRequirements >
        <ClashRequirement name="(&string;)"
                maximum_clashes_allowed="(0 &non_negative_integer;)"
                clash_radius="(4.0 &real;)" />
        <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 &real;)" />
        <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 &real;)" />
        <NonTerminalStartingSegmentRequirement />
        <SizeInSegmentsRequirement name="(&string;)"
                maximum_size="(10000 &non_negative_integer;)"
                minimum_size="(0 &non_negative_integer;)" />
    </AssemblyRequirements>
</AssemblyMover>

start_temperature: Temperature at start of simulated annealing
end_temperature: Temperature at end of simulated annealing
add_probability: Probability of adding a triplet of segments at any given step during assembly
delete_probability: Probability of deleting a terminal triplet of segments at any given step during assembly
conformer_switch_probability: Probability of switching ligand conformers during assembly. This should only be used if a ligand is present AND if you have provided conformers for that ligand.
window_width: Required number of overlapping residues for two segments to be considered a match. Used in hashless SEWING only (for hashed SEWING, this is determined by the hasher settings used when generating the edge file).
minimum_cycles: Minimum number of Monte Carlo cycles for assembly before completion requirements are checked.
maximum_cycles: Maximum number of Monte Carlo cycles for assembly before forced termination.
model_file_name: (REQUIRED) Path to file defining segments to use during assembly
hashed: Use the hasher during assembly to check overlap of all atoms? Requires an input edge file.
edge_file_name: Path to edge file to use during assembly (only used if hashed is set to true)
max_segments: Maximum number of segments to include in the final assembly
max_segment_length: Maximum number of residues to include in a segment
output_pose_per_move: Setting to true will output a pose after each move/revert.
recover_lowest_assembly: Setting to true will output the lowest assembly in the final pose

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

weight: How heavily will this term be weighted during scoring?

Subtag IntraDesignTerminusMotifScorer: Motif score to measure packing of assembly against partner PDB

weight: How heavily will this term be weighted during scoring?
optimum_distance: How far apart should that residue optimally be from the terminus?
maximum_unpenalized_variance: How far off from that can it be before it should be penalized?

Subtag LigandScorer: Scores how well ligand is buried based on orientation of nearby Ca's

weight: How heavily will this term be weighted during scoring?
ligand_interaction_cutoff_distance: The distance cutoff between ligand atom and c alpha that is considered an interaction.

Subtag MotifScorer: Basic Motif score among all helices

weight: How heavily will this term be weighted during scoring?

Subtag PartnerMotifScorer: Motif score to measure packing of assembly against partner PDB

weight: How heavily will this term be weighted during scoring?

Subtag SegmentContactOrderScorer: Favors assemblies whose segments form contacts with segments distant in the assembly

weight: How heavily will this term be weighted during scoring?

Subtag StartingNodeMotifScorer: Specifically scores packing against the starting node

weight: How heavily will this term be weighted during scoring?

Subtag SubsetPartnerMotifScorer: Motif score to measure packing of assembly against partner PDB

weight: How heavily will this term be weighted during scoring?
region_start: What is the first residue of the scored subset?
region_end: What is the last residue of the scored subset?

Subtag TerminusMotifScorer: Motif score to measure packing of assembly against partner PDB

weight: How heavily will this term be weighted during scoring?
partner_residue: Which residue of the partner should this scorer calculate distance to?
optimum_distance: How far apart should that residue optimally be from the terminus?
maximum_unpenalized_variance: How far off from that can it be before it should be penalized?
terminus: Which terminus should be scored?

Subtag TopNMotifScorer: Basic Motif score among all helices

weight: How heavily will this term be weighted during scoring?
scores_to_keep: How many scores from each pair should be counted?

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

maximum_clashes_allowed: Maximum number of clashes to allow in the assembly
clash_radius: Radius in Angstroms within which two residues are considered to be clashing

Subtag DsspSpecificLengthRequirement: Restricts the number of residues in segments with the specified DSSP

dssp_code: DSSP code whose length the requirement is restricting
maximum_length: Maximum number of residues in a segment with the given secondary structure
minimum_length: Minimum number of residues in a segment with the given secondary structure

Subtag KeepLigandContactsRequirement: Fails if an assembly's ligands lose more than a set number of contacts

contact_distance_cutoff: Maximum distance between two contact atoms before the contact is considered broken

Subtag LengthInResiduesRequirement: Checks the number of segments in the assembly

maximum_length: Maximum number of residues to allow in the assembly
minimum_length: Minimum number of residues in the final assembly

Subtag LigandClashRequirement: Checks for clashes between the assembly and its ligands

maximum_clashes_allowed: Maximum number of clashes to allow in the assembly
clash_radius: Radius in Angstroms within which two residues are considered to be clashing

Subtag SizeInSegmentsRequirement: Checks the number of segments in the assembly

maximum_size: Maximum number of secondary structure elements (including loops) to allow in the assembly
minimum_size: Minimum number of secondary structure elements (including loops) in the final assembly

scripting_documentation/RosettaScripts/xsd/mover_AssemblyMover_type