Autogenerated Tag Syntax Documentation:

Author: Jared Adolf-Bryfogle ( @brief Simple mover to Create a sequence motif in a region of protein using the SequenceMotifTaskOperation. Uses psueo-regular expressions to define the motif.

@details Simply calls the packer using the operation, optionally packing neighbor residues as it does so. If you need something more complex, use the SequenceMotifTaskOperation directly.

<CreateSequenceMotifMover name="(&string;)" motif="(&string;)"
        pack_neighbors="(true &bool;)" design_neighbors="(false &bool;)"
        neighbor_distance="(6.0 &real;)"
        pack_rounds="(5 &non_negative_integer;)" residue_selector="(&string;)"
        scorefxn="(&string;)" />
  • motif: This is slightly similar to a regex, but not quite. We are not matching a sequence, we are designing in a motif regardless of the current sequence, anywhere in a protein.

    • Each letter corresponds to a position. Using [ ] indicates a more complicated expression for that position.
    • An X indicates it can be anything, and that we are designing here.
    • An AA Letter, like V, indicates that that position will be designed to a V.
    • A - charactor indicates that that position stays with whatever it is currently. We essentially skip this position.
    • An expression like: [^PAV] indicates that we will design anything except Proline, Alanine, and Valine
    • An expression like: [NTS] indicates that that position can be Asparigine, Threonine, or Serine and only of these will be enabled during the design.
    • RESFILE commands are accepted as well. These require a % charactor in from of the whole expression. For example [%POLAR] would set that position to only polar design.

    EXAMPLE: Glycosylation N-Linked motif design: N[^P][ST]

  • pack_neighbors: Should we pack the neighboring residues to the motif during design?
  • design_neighbors: Should we design the neighboring residues to the motif during design?
  • neighbor_distance: Packing distance to neighbors?
  • pack_rounds: Number of rounds to run packing/design.
  • residue_selector: The name of the already defined ResidueSelector that will be used by this object
  • scorefxn: Name of score function to use