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Mover created by Labonte JWLabonte@jhu.edu.

Description

A Mover for flipping the plane of a carbohydrate pyranose ring 180 degrees about its anomeric bond.

Based on a given ResidueSelector and limited by a MoveMap, this Mover selects applicable cyclic residues and performs a 180-degree shearing move in which the anomeric bond and the main-chain bond on the opposite side of the ring are moved in opposite directions. An "applicable" residue is limited to 1,4-linked aldopyranoses or 2,5-linked ketopyranoses for which both the anomeric bond and the glycosidic linkage bond are equatorial.

This Mover is useful in cases — for example, when working with highly charged and sulfated heparins — where Rosetta models an oligo- or polysaccharide in such a way that the residue is sitting in the relatively correct position but is missing favorable interactions that it could make on the other side of the glycan ring. Sometimes, a simple "ring flip" could correct this, but the energy barrier to rotate is too high; the small moves of a ShearMover would never flip the ring around.

RosettaScripts Details

Autogenerated Tag Syntax Documentation:

Based on a given ResidueSelector and limited by a MoveMap, this mover selects applicable cyclic residues and performs a 180-degree shearing move in which the anomeric bond and the main-chain bond on the opposite side of the ring are moved in opposite directions.

References and author information for the RingPlaneFlipMover mover:

RingPlaneFlipMover Mover's author(s): Jason W. Labonte, Department of Chemistry, Johns Hopkins University, Baltimore, MD [JWLabonte@jhu.edu]

<RingPlaneFlipMover name="(&string;)" residue_selector="(&string;)"
        movemap_factory="(&string;)" >
    <MoveMap name="(&string;)" bb="(&bool;)" chi="(&bool;)" jump="(&bool;)" >
        <Jump number="(&non_negative_integer;)" setting="(&bool;)" />
        <Chain number="(&non_negative_integer;)" chi="(&bool;)" bb="(&bool;)" />
        <Span begin="(&non_negative_integer;)" end="(&non_negative_integer;)"
                chi="(&bool;)" bb="(&bool;)" bondangle="(&bool;)" bondlength="(&bool;)" />
        <ResidueSelector selector="(&string;)" chi="(&bool;)" bb="(&bool;)"
                bondangle="(&bool;)" bondlength="(&bool;)" />
    </MoveMap>
</RingPlaneFlipMover>
  • residue_selector: The name of a pre-defined ResidueSelector. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.
  • movemap_factory: The name of a pre-defined MoveMapFactory.

Subtag MoveMap: MoveMap specification

  • bb: move backbone torsions?
  • chi: move sidechain chi torsions?
  • jump: move all jumps?

Subtag Jump: jumps are the not-chemistry internal coordinate connections between separate parts of your pose

  • number: (REQUIRED) Which jump number (in the FoldTree)
  • setting: (REQUIRED) true for move, false for don't move

Subtag Chain: this controls a kinematically contiguous chain (think protein chains)

  • number: (REQUIRED) which chain?
  • chi: (REQUIRED) move sidechain chi torsions?
  • bb: (REQUIRED) move backbone torsions?

Subtag Span: XRW TO DO, probably a user-defined region of the Pose

  • begin: (REQUIRED) beginning of span
  • end: (REQUIRED) end of span
  • chi: (REQUIRED) move sidechain chi torsions?
  • bb: (REQUIRED) move backbone torsions?
  • bondangle: move 3-body angles?
  • bondlength: move 2-body lengths?

Subtag ResidueSelector: Residue selector defined region of the Pose.

  • selector: (REQUIRED) Residue selector
  • chi: (REQUIRED) move sidechain chi torsions?
  • bb: (REQUIRED) move backbone torsions?
  • bondangle: move 3-body angles?
  • bondlength: move 2-body lengths?

See Also