MinMover

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MinMover

Autogenerated Tag Syntax Documentation:

Does minimization over sidechain and/or backbone

<MinMover name="(&string;)" jump="(&string;)"
        abs_score_convergence_threshold="(&real;)"
        max_iter="(200 &non_negative_integer;)"
        type="(lbfgs_armijo_nonmonotone &minimizer_type;)"
        tolerance="(0.01 &real;)" cartesian="(false &bool;)"
        bondangle="(0 &bool;)" bondlength="(0 &bool;)" chi="(&bool;)"
        bb="(&bool;)" omega="(true &bool;)"
        bb_task_operations="(&task_operation_comma_separated_list;)"
        chi_task_operations="(&task_operation_comma_separated_list;)"
        bondangle_task_operations="(&task_operation_comma_separated_list;)"
        bondlength_task_operations="(&task_operation_comma_separated_list;)"
        movemap_factory="(&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>
</MinMover>

jump: Comma-separated list of jumps to minimize over (be sure this jump exists!). If set to "ALL", all jumps will be set to minimize. If set to "0", jumps will be set not to minimize
abs_score_convergence_threshold: Keep minimizing until difference before minimization is less than this threshold
max_iter: maximum number of iterations allowed. This default is also very loose. This and the tolerance setting both affect if you will reach convergence
type: Minimizer type. linmin, dfpmin, dfpmin_armijo, dfpmin_armijo_nonmonotone. dfpmin minimzers can also be used with absolute tolerance (add "atol" to the minimizer type).
tolerance: Criteria for convergence of minimization. The default is very loose, it's recommended to specify something less than 0.01. max_iter also affects convergence
cartesian: Perform cartesian minimization?
bondangle: Minimize bond angles?
bondlength: Minimize bond lengths?
chi: Minimize chi angles?
bb: Minimize backbone torsion angles?
omega: Minimize omega torsions?
bb_task_operations: Task operations specifying residues for backbone minimization
chi_task_operations: Task operations specifying residues for sidechain minimization
bondangle_task_operations: Task operations specifying residues for bond angle minimization
bondlength_task_operations: Task operation specifying residues for bond length minimization
movemap_factory: The name of the already-defined MoveMapFactory that will be used to alter the default behavior of the MoveMap. By default, all backbone, chi, and jump DOFs are allowed to change. A MoveMapFactory can be used to change which of those DOFs are actually enabled. Be warned that combining a MoveMapFactory with a MoveMap can result in unexpected behavior.
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?

Notes:

cartesian: To set up a score function for Cartesian minimization (i.e if you get the ERROR: Scorefunction not set up for nonideal/Cartesian scoring) you must set cart_bonded to 0.5 and pro_close to 0.0.
MoveMap: The movemap can be programmed down to individual degrees of freedom. See FastRelax for more details.

MinMover

MinMover

Notes:

See Also