PerturbBundle

Documentation by Vikram K. Mulligan (vmullig@uw.edu). Last updated 12 October 2018.

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PerturbBundle

This mover operates on a pose generated with the MakeBundle or BundleGridSampler movers. It perturbs (i.e. adds a small, random value to) one or more Crick parameters, then alters the backbone conformation to reflect the altered Crick parameters. This is useful for iterative Monte Carlo searches of Crick parameter space. The mover can also set the absolute value of a parameter directly (i.e. without random perturbation)

Usage

Autogenerated Tag Syntax Documentation:

Perturb helical bundles by direct manipulation of their bundle parameters

References and author information for the PerturbBundle mover:

PerturbBundle Mover's author(s): Vikram K. Mulligan, Systems Biology, Center for Computational Biology, Flatiron Institute [vmulligan@flatironinstitute.org]

<PerturbBundle name="(&string;)" use_degrees="(false &bool;)"
        default_perturbation_type="(&pert_type;)" r0="(0.000000 &real;)"
        r0_perturbation="(0.0 &real;)"
        r0_perturbation_type="(gaussian &string;)" omega0="(0.000000 &real;)"
        omega0_perturbation="(0.0 &real;)"
        omega0_perturbation_type="(gaussian &string;)"
        delta_omega0="(0.000000 &real;)"
        delta_omega0_perturbation="(0.0 &real;)"
        delta_omega0_perturbation_type="(gaussian &string;)"
        delta_omega1="(0.000000 &real;)"
        delta_omega1_perturbation="(0.0 &real;)"
        delta_omega1_perturbation_type="(gaussian &string;)"
        delta_t="(0.000000 &real;)" delta_t_perturbation="(0.0 &real;)"
        delta_t_perturbation_type="(gaussian &string;)"
        z0_offset="(0.000000 &real;)" z0_offset_perturbation="(0.0 &real;)"
        z0_offset_perturbation_type="(gaussian &string;)"
        z1_offset="(0.000000 &real;)" z1_offset_perturbation="(0.0 &real;)"
        z1_offset_perturbation_type="(gaussian &string;)"
        epsilon="(1.000000 &real;)" epsilon_perturbation="(0.0 &real;)"
        epsilon_perturbation_type="(gaussian &string;)"
        repeating_unit_offset="(0 &non_negative_integer;)"
        r1_peratom="(0 &real_wsslist;)" omega1="(0.000000 &real;)"
        omega1_perturbation="(0.0 &real;)"
        omega1_perturbation_type="(gaussian &string;)" z1="(0.000000 &real;)"
        z1_perturbation="(0.0 &real;)"
        z1_perturbation_type="(gaussian &string;)"
        delta_omega1_peratom="(0 &real_wsslist;)"
        delta_z1_peratom="(0 &real_wsslist;)" invert="(false &bool;)"
        set_dihedrals="(true &bool;)" set_bondangles="(true &bool;)"
        set_bondlengths="(true &bool;)" >
    <Helix helix_index="(&positive_integer;)" r0="(0.000000 &real;)"
            r0_perturbation="(0.0 &real;)"
            r0_perturbation_type="(gaussian &string;)"
            r0_copies_helix="(0 &non_negative_integer;)" omega0="(0.000000 &real;)"
            omega0_perturbation="(0.0 &real;)"
            omega0_perturbation_type="(gaussian &string;)"
            omega0_copies_helix="(0 &non_negative_integer;)"
            pitch_from_helix="(0 &non_negative_integer;)"
            delta_omega0="(0.000000 &real;)"
            delta_omega0_perturbation="(0.0 &real;)"
            delta_omega0_perturbation_type="(gaussian &string;)"
            delta_omega0_copies_helix="(0 &non_negative_integer;)"
            delta_omega1="(0.000000 &real;)"
            delta_omega1_perturbation="(0.0 &real;)"
            delta_omega1_perturbation_type="(gaussian &string;)"
            delta_omega1_copies_helix="(0 &non_negative_integer;)"
            delta_t="(0.000000 &real;)" delta_t_perturbation="(0.0 &real;)"
            delta_t_perturbation_type="(gaussian &string;)"
            delta_t_copies_helix="(0 &non_negative_integer;)"
            z0_offset="(0.000000 &real;)" z0_offset_perturbation="(0.0 &real;)"
            z0_offset_perturbation_type="(gaussian &string;)"
            z0_offset_copies_helix="(0 &non_negative_integer;)"
            z1_offset="(0.000000 &real;)" z1_offset_perturbation="(0.0 &real;)"
            z1_offset_perturbation_type="(gaussian &string;)"
            z1_offset_copies_helix="(0 &non_negative_integer;)"
            epsilon="(1.000000 &real;)" epsilon_perturbation="(0.0 &real;)"
            epsilon_perturbation_type="(gaussian &string;)"
            epsilon_copies_helix="(0 &non_negative_integer;)"
            repeating_unit_offset="(0 &non_negative_integer;)"
            r1_peratom="(0 &real_wsslist;)" omega1="(0.000000 &real;)"
            omega1_perturbation="(0.0 &real;)"
            omega1_perturbation_type="(gaussian &string;)"
            omega1_copies_helix="(0 &non_negative_integer;)" z1="(0.000000 &real;)"
            z1_perturbation="(0.0 &real;)"
            z1_perturbation_type="(gaussian &string;)"
            z1_copies_helix="(0 &non_negative_integer;)"
            delta_omega1_peratom="(0 &real_wsslist;)"
            delta_z1_peratom="(0 &real_wsslist;)" invert="(false &bool;)"
            set_dihedrals="(true &bool;)" set_bondangles="(true &bool;)"
            set_bondlengths="(true &bool;)" />
</PerturbBundle>

use_degrees: Interpret user-supplied angles as degrees rather than radians
default_perturbation_type: Default type for perturbations to the bundle parameters, either uniform or gaussian
r0: Major helix radius, in Angstroms.
r0_perturbation: Perturbation magnitude for perturbing r0.
r0_perturbation_type: Perturbation type for perturbing r0. Can be "gaussian" or "uniform".
omega0: Major helix twist per residue, stored in radians.
omega0_perturbation: Perturbation magnitude for perturbing omega0.
omega0_perturbation_type: Perturbation type for perturbing omega0. Can be "gaussian" or "uniform".
delta_omega0: Rotation of a helix about the z-axis, stored in radians.
delta_omega0_perturbation: Perturbation magnitude for perturbing delta_omega0.
delta_omega0_perturbation_type: Perturbation type for perturbing delta_omega0. Can be "gaussian" or "uniform".
delta_omega1: Rotation of a helix about its own axis, stored in radians.
delta_omega1_perturbation: Perturbation magnitude for perturbing delta_omega1.
delta_omega1_perturbation_type: Perturbation type for perturbing delta_omega1. Can be "gaussian" or "uniform".
delta_t: Offset along the polypeptide backbone, in residues.
delta_t_perturbation: Perturbation magnitude for perturbing delta_t.
delta_t_perturbation_type: Perturbation type for perturbing delta_t. Can be "gaussian" or "uniform".
z0_offset: Offset along the global z-axis, in Angstroms.
z0_offset_perturbation: Perturbation magnitude for perturbing z0_offset.
z0_offset_perturbation_type: Perturbation type for perturbing z0_offset. Can be "gaussian" or "uniform".
z1_offset: Offset along the superhelical path through space, in Angstroms.
z1_offset_perturbation: Perturbation magnitude for perturbing z1_offset.
z1_offset_perturbation_type: Perturbation type for perturbing z1_offset. Can be "gaussian" or "uniform".
epsilon: Lateral squash parameter/eccentricity of the cross-section of a bundle or barrel.
epsilon_perturbation: Perturbation magnitude for perturbing epsilon.
epsilon_perturbation_type: Perturbation type for perturbing epsilon. Can be "gaussian" or "uniform".
repeating_unit_offset: Shift, in residues, of the repeating unit of a helix.
r1_peratom: Minor helix radius -- a vector of real numbers in Angstroms, with one per atom in the repeating unit of a helix. Read from Crick params file, and not normally set by hand.
omega1: Minor helix twist per residue, stored in radians. Read from Crick params file, and not normally set by hand, sampled, or perturbed.
omega1_perturbation: Perturbation magnitude for perturbing omega1.
omega1_perturbation_type: Perturbation type for perturbing omega1. Can be "gaussian" or "uniform".
z1: Minor helix rise per residue along the helix axis, in Angstroms. Read from Crick params file, and not normally set by hand, sampled, or perturbed.
z1_perturbation: Perturbation magnitude for perturbing z1.
z1_perturbation_type: Perturbation type for perturbing z1. Can be "gaussian" or "uniform".
delta_omega1_peratom: Minor helix angular offsets of each mainchain atom in the repeating unit, in radians. Read from Crick params file, and not normally set by hand.
delta_z1_peratom: Minor helix axial offsets of each mainchain atom in the repeating unit, in Angstroms. Read from Crick params file, and not normally set by hand.
invert: Inversion state of this helix -- true for inverted.
set_dihedrals: True indicates that the parametric machinery will set mainchain torsion values.
set_bondangles: True indicates that the parametric machinery will allow mainchain bond angle values to deviate from ideality.
set_bondlengths: True indicates that the parametric machinery will allow mainchain bond length values to deviate from ideality.

Subtag Helix:

helix_index: (REQUIRED) Numerical index for this particular helix
r0: Major helix radius, in Angstroms.
r0_perturbation: Perturbation magnitude for perturbing r0.
r0_perturbation_type: Perturbation type for perturbing r0. Can be "gaussian" or "uniform".
r0_copies_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which the value for r0 should be copied.
omega0: Major helix twist per residue, stored in radians.
omega0_perturbation: Perturbation magnitude for perturbing omega0.
omega0_perturbation_type: Perturbation type for perturbing omega0. Can be "gaussian" or "uniform".
omega0_copies_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which the value for omega0 should be copied.
pitch_from_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which pitch value should be copied in order to set omega0, the twist per residue. An alternative to "omega0_copies_helix".
delta_omega0: Rotation of a helix about the z-axis, stored in radians.
delta_omega0_perturbation: Perturbation magnitude for perturbing delta_omega0.
delta_omega0_perturbation_type: Perturbation type for perturbing delta_omega0. Can be "gaussian" or "uniform".
delta_omega0_copies_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which the value for delta_omega0 should be copied.
delta_omega1: Rotation of a helix about its own axis, stored in radians.
delta_omega1_perturbation: Perturbation magnitude for perturbing delta_omega1.
delta_omega1_perturbation_type: Perturbation type for perturbing delta_omega1. Can be "gaussian" or "uniform".
delta_omega1_copies_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which the value for delta_omega1 should be copied.
delta_t: Offset along the polypeptide backbone, in residues.
delta_t_perturbation: Perturbation magnitude for perturbing delta_t.
delta_t_perturbation_type: Perturbation type for perturbing delta_t. Can be "gaussian" or "uniform".
delta_t_copies_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which the value for delta_t should be copied.
z0_offset: Offset along the global z-axis, in Angstroms.
z0_offset_perturbation: Perturbation magnitude for perturbing z0_offset.
z0_offset_perturbation_type: Perturbation type for perturbing z0_offset. Can be "gaussian" or "uniform".
z0_offset_copies_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which the value for z0_offset should be copied.
z1_offset: Offset along the superhelical path through space, in Angstroms.
z1_offset_perturbation: Perturbation magnitude for perturbing z1_offset.
z1_offset_perturbation_type: Perturbation type for perturbing z1_offset. Can be "gaussian" or "uniform".
z1_offset_copies_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which the value for z1_offset should be copied.
epsilon: Lateral squash parameter/eccentricity of the cross-section of a bundle or barrel.
epsilon_perturbation: Perturbation magnitude for perturbing epsilon.
epsilon_perturbation_type: Perturbation type for perturbing epsilon. Can be "gaussian" or "uniform".
epsilon_copies_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which the value for epsilon should be copied.
repeating_unit_offset: Shift, in residues, of the repeating unit of a helix.
r1_peratom: Minor helix radius -- a vector of real numbers in Angstroms, with one per atom in the repeating unit of a helix. Read from Crick params file, and not normally set by hand.
omega1: Minor helix twist per residue, stored in radians. Read from Crick params file, and not normally set by hand, sampled, or perturbed.
omega1_perturbation: Perturbation magnitude for perturbing omega1.
omega1_perturbation_type: Perturbation type for perturbing omega1. Can be "gaussian" or "uniform".
omega1_copies_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which the value for omega1 should be copied.
z1: Minor helix rise per residue along the helix axis, in Angstroms. Read from Crick params file, and not normally set by hand, sampled, or perturbed.
z1_perturbation: Perturbation magnitude for perturbing z1.
z1_perturbation_type: Perturbation type for perturbing z1. Can be "gaussian" or "uniform".
z1_copies_helix: The index of the parametric object (e.g. the helix, in the case of a helical bundle) from which the value for z1 should be copied.
delta_omega1_peratom: Minor helix angular offsets of each mainchain atom in the repeating unit, in radians. Read from Crick params file, and not normally set by hand.
delta_z1_peratom: Minor helix axial offsets of each mainchain atom in the repeating unit, in Angstroms. Read from Crick params file, and not normally set by hand.
invert: Inversion state of this helix -- true for inverted.
set_dihedrals: True indicates that the parametric machinery will set mainchain torsion values.
set_bondangles: True indicates that the parametric machinery will allow mainchain bond angle values to deviate from ideality.
set_bondlengths: True indicates that the parametric machinery will allow mainchain bond length values to deviate from ideality.

Default options for all helices are set in the PerturbBundle tag. A default perturber type for all perturbations can be set with the default_perturbation_type option; currently-accepted values are "gaussian" and "uniform". These can be overridden on a parameter-by-parameter basis with individual perturbation_type options. Default perturbation magnitudes are set with options ending in _perturbation. If an option is omitted, that Crick parameter is not perturbed. These can also be overridden on a helix-by-helix basis by adding Helix sub-tags. In the sub-tags, if an option is omitted, that degree of freedom is not perturbed unless a default perturbation was set for it in the main tag. In the sub-tags, helices can also be set to copy degrees of freedom of other helices with copies_helix options. A special case of this is the pitch_copies_helix option, which will set omega0 to whatever value is necessary to ensure that one helix copies the major helix pitch (the rise along the major helix axis per turn about the major helix axis) of another helix.

As of 24 May 2017, this mover can also be used to set the value of a parameter to a desired absolute value. To set the value of epsilon to 0.75, for example, one would use epsilon="0.75" (which would be used in lieu of an epsilon_perturbation option).

PerturbBundle

PerturbBundle

Usage

See Also