Page created by Vikram K. Mulligan (vmulligan@flatironinstitute.org). Last modified 12 October 2018. Back to Movers page
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.
<PerturbBundle name=(&string) default_perturbation_type=(&string)
r0_perturbation=(&real) r0_perturbation_type=(&string)
omega0_perturbation=(&real) omega0_perturbation_type=(&string)
delta_omega0_perturbation=(&real) delta_omega0_perturbation_type=(&string)
delta_omega1_perturbation=(&real) delta_omega1_perturbation_type=(&string)
delta_t_perturbation=(&real) delta_t_perturbation_type=(&string) >
<Helix helix_index=(&int)
r0_perturbation=(&real) r0_perturbation_type=(&string) r0_copies_helix=(&int)
omega0_perturbation=(&real) omega0_perturbation_type=(&string) omega0_copies_helix=(&int)
delta_omega0_perturbation=(&real) delta_omega0_perturbation_type=(&string) delta_omega0_copies_helix=(&int)
delta_omega1_perturbation=(&real) delta_omega1_perturbation_type=(&string) delta_omega1_copies_helix=(&int)
delta_t_perturbation=(&real) delta_t_perturbation_type=(&string) delta_t_copies_helix=(&int) />
</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 _perturbation options. 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. 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.