PertMinMover

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PertMinMover

Autogenerated Tag Syntax Documentation:

Do a Roberto Chica inspired random atom coordinate perturbation followed by (Cartesian) minimization.

<PertMinMover name="(&string;)" pert_size="(0.001 &real;)"
        uniform="(true &bool;)" sc_only="(false &bool;)"
        residue_selector="(&string;)" scorefxn="(&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>
</PertMinMover>

pert_size: How large a perturbation to make
uniform: Do the perturbation in a uniform sphere, rather than Gaussian
sc_only: Only do the perturbations on sidechain atoms (not backbone)
residue_selector: . 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.
scorefxn: Name of score function to use

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?

This mover is based off the approach taken by Davey & Chica, Proteins 82:771-784 https://onlinelibrary.wiley.com/doi/full/10.1002/prot.24457

In short, it explores local conformational space by making a small, random Cartesian perturbation of atomic coordinates, followed by an energy minimization. In a rough energy landscape, even small variations in starting position can greatly change the trajectory of minimization and the final result, resulting in local conformation search (see Fig. 2 of Davey & Chica).

In contrast to the Davey & Chica approach, which used a fixed +/- 0.001 Ang perturbation in the PDB file, this mover allows you to vary the size and distribution of the perturbation, either applying a displacement selected uniformly within in a sphere of a given radius (the default), or from a spherically symmetric Gaussian distribution of a given standard deviation (which biases toward smaller displacements while allowing much larger ones).

Which atoms are perturbed can be controlled by the provided ResidueSelector (defaults to all residues in the system), and the sc_only flag. Which degrees of freedom can move during minimization can be controlled by the provided MoveMap specification.

PertMinMover

PertMinMover

See Also