Documentation by Vikram K. Mulligan (vmullig@uw.edu). Last updated 24 May 2017.

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## PerturbBundle

This mover operates on a pose generated with the MakeBundle mover. 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)

<PerturbBundle name=(&string) use_degrees=(false &bool) default_perturbation_type=(&string)
r0_perturbation=(&real) r0_perturbation_type=(&string) r0=(&real)
omega0_perturbation=(&real) omega0_perturbation_type=(&string) omega0=(&real)
delta_omega0_perturbation=(&real) delta_omega0_perturbation_type=(&string) delta_omega0=(&real)
delta_omega1_perturbation=(&real) delta_omega1_perturbation_type=(&string) delta_omega1=(&real)
delta_t_perturbation=(&real) delta_t_perturbation_type=(&string) delta_t=(&real)
z1_offset_perturbation=(&real) z1_offset_perturbation_type=(&string) z1_offset=(&real)
z0_offset_perturbation=(&real) z0_offset_perturbation_type=(&string) z0_offset=(&real)
epsilon_perturbation=(&real) epsilon_perturbation_type=(&string) epsilon=(&real)
>
<Helix helix_index=(&int)
r0_perturbation=(&real) r0_perturbation_type=(&string) r0_copies_helix=(&int) r0=(&real)
omega0_perturbation=(&real) omega0_perturbation_type=(&string) omega0_copies_helix=(&int) pitch_from_helix=(&int) omega0=(&real)
delta_omega0_perturbation=(&real) delta_omega0_perturbation_type=(&string) delta_omega0_copies_helix=(&int) delta_omega0=(&real)
delta_omega1_perturbation=(&real) delta_omega1_perturbation_type=(&string) delta_omega1_copies_helix=(&int) delta_omega1=(&real)
delta_t_perturbation=(&real) delta_t_perturbation_type=(&string) delta_t_copies_helix=(&int)
z1_offset_perturbation=(&real) z1_offset_perturbation_type=(&string) z1_offset_copies_helix=(&int) z1_offset=(&real)
z0_offset_perturbation=(&real) z0_offset_perturbation_type=(&string) z0_offset_copies_helix=(&int) z0_offset=(&real)
epsilon_perturbation=(&real) epsilon_perturbation_type=(&string) epsilon_copies_helix=(&int)  epsilon=(&real)
/>
</PerturbBundle>


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. Perturbable Crick parameters include:

r0: The major helix radius.
omega0: The major helix twist per residue.
delta_omega0: The radial offset about the major helix axis.
delta_omega1: The rotation of the minor helix about the minor helix axis.
delta_t: A value to offset the helix by a certain number of amino acid residues along its direction of propagation (i.e. along the helix-of-helices path through space).
z1_offset: A value to offset the helix by a certain number Angstroms along the minor helix axis (i.e. a helical path through space). Note that the distance is measured along the z-axis (not along the helical path). Inverted helices are shifted in the opposite direction.
z0_offset: A value to offset the helix by a certain number Angstroms along the major helix axis (i.e. a straight path through space). Inverted helices are shifted in the opposite direction.
epsilon: A value to squash the bundle laterally, which is useful for generating beta-barrels. A value of 1.0 (the default) yields a bundle with a circular cross-section, and simplifies the generating equations to the original Crick equations. A value between 0.5 and 1.0 is recommended for a slightly squashed bundle or beta-barrel. The cross section is not a true ellipse, but rather the shape that results from the expression r=(1-epsilon)/2*(cos(2*theta)+1)+epsilon, where r is the radius and theta is the angle to the x-axis. Values outside of the range [0.5,1.0] are not recommended.

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).