MergePDBMover

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MergePDBMover

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Overview

Combines two poses along a common secondary structure element and redesigns the sequence as appropriate.

<MergePDB name="(&string;)" symm_file="(&string;)"
        attachment_termini="(n_term &attachment_termini_type;)"
        chain="(A &string;)" overlap_length="(4 &non_negative_integer;)"
        overlap_rmsd="(0.3 &real;)"
        overlap_scan_range_cmdLine_pose="(20 &non_negative_integer;)"
        overlap_scan_range_xml_pose="(20 &non_negative_integer;)"
        attach_pdb="(&string;)" design_range="(9 &real;)"
        packing_range="(8 &real;)" detect_disulf_before_pack="(true &bool;)"
        do_minimize="(true &bool;)" no_design_label="(&string;)"
        duplicate_rmsd_pose_threshold="(1.0 &real;)"
        init_overlap_sequence="[input_pose|xml_pose|both]"
        scorefxn="(&string;)" output_only_first="(false &bool;)"
        output_overlap_positions="(false &bool;)" do_design="(true &bool;)"
        clash_threshold="(10 &real;)"
        task_operations="(&task_operation_comma_separated_list;)"
        packer_palette="(&named_packer_palette;)" />

Options:

task_operations: By default, any residue within packing_range will be repacked and any residue within design_range designed.
scorefxn: The score function used for design and packing. Required if not being used as a subtag within some other LoopMover.
attachment_termini: [n_term or c_term] do you want the xml_pose attached to the n_term or c_term of the input_pose (-in:file:s pose)
attach_pdb: pdb to attach
overlap_length: Number of residues that overlap
overlap_rmsd: cutoff for what is considered an overlap
design_range: distance in ang from the overlap that is being designed
packing_range: distance from the designed residues that is allowed to pack
overlap_scan_range_cmdLine_pose: how many residues on the -in:file pdb that are checked for overlap
overlap_scan_range_xml_pose: how many residue on the attach_pdb are checked for overlap
symm_file: if using symmetry(input pose symmetric) must rebuild symmetry after overlap. Give a path to the symmetry definition
no_design_label: Use the add_residue_label to define parts you don't want designed
init_overlap_sequence:[input_pose|xml_pose|both]: which pose do you want initialize the overlap rotamers
duplicate_rmsd_pose_threshold: rmsd for eliminating duplicate poses. For speed does not work >1.0
chain: Which chain to operate on. Defaults to 'A'.
do_design: Perform sequence design (default:true)
do_minimize: Perform energy minimization (default:true)

Notes:

PDBInfoLabels are added to the output pose:

overlap - residues that are superimposed from input_pose and xml_pose

other_overlap - residues that were detected around the design_range that were designed

other_overlap_sym - residues that were detected by symmetry that were designed

Caveats:

The pose must start symmetric to use the symm_file option.
if no_design_label is defined you must use the (default)init_overlap_sequence="input_pose"(default)