BundleGridSampler

Page created by Vikram K. Mulligan (vmulligan@flatironinstitute.org). Last modified 12 October 2018. Back to Movers page

Table of Contents

- BundleGridSampler
  - Description
  - See also

BundleGridSampler

Description

Generates a helical bundle, sampling user-specified ranges of parameters and outputting the lowest-energy bundle encountered (and its accompanying parameter values). Optionally, this mover can also output PDB files for all bundle geometries sampled. Note that because a strand is a special case of a helix, this mover can also be used to sample beta-barrel conformations or mixed alpha-beta structures.

<BundleGridSampler name=(&string) symmetry=(0 &int) symmetry_copies=(0 &int) set_dihedrals=(true &bool)
   set_bondlengths=(false &bool) set_bondangles=(false &bool) residue_name=("ALA" &string)
   crick_params_file=("alpha_helix" &string)  helix_length=(0 &int) invert=(false &bool)
   scorefxn=(&string) selection_type=("low"||"high" &string) pre_selection_mover=(&string)
   dump_pdbs=(false &bool) pdb_prefix=("bgs_out" &string) max_samples=(10000 &int)
    r0=(&real) OR ( r0_min=(&real) r0_max=(&real) r0_samples=(&int) )
    omega0=(&real) OR ( omega0_min=(&real) omega0_max=(&real) omega0_samples=(&int) )
    delta_omega0=(&real) OR ( delta_omega0_min=(&real) delta_omega0_max=(&real) delta_omega0_samples=(&int) )
    delta_omega1=(&real) OR ( delta_omega1_min=(&real) delta_omega1_max=(&real) delta_omega1_samples=(&int) )
    delta_t=(&real) OR ( delta_t_min=(&real) delta_t_max=(&real) delta_t_samples=(&int) )
   >
   <Helix set_dihedrals=(true &bool) set_bondlengths=(false &bool) set_bondangles=(false &bool) invert=(false &bool)
     residue_name=("ALA" &string) crick_params_file=("alpha_helix" &string) helix_length=(0 &int)
     r0=(&real) OR (r0_copies_helix=(&int)) OR ( r0_min=(&real) r0_max=(&real) r0_samples=(&int) )
     omega0=(&real) OR (omega0_copies_helix=(&int)) OR ( omega0_min=(&real) omega0_max=(&real) omega0_samples=(&int) )
     delta_omega0=(&real) OR (delta_omega0_copies_helix=(&int)) OR ( delta_omega0_min=(&real) delta_omega0_max=(&real) delta_omega0_samples=(&int) )
     delta_omega1=(&real) OR (delta_omega1_copies_helix=(&int)) OR ( delta_omega1_min=(&real) delta_omega1_max=(&real) delta_omega1_samples=(&int) )
     delta_t=(&real) OR (delta_t_copies_helix=(&int)) OR ( delta_t_min=(&real) delta_t_max=(&real) delta_t_samples=(&int) )
   >
   <Helix ...>
   <Helix ...>
   ...
</BundleGridSampler>

Default parameter values or parameter ranges are set in the BundleGridSampler tag, and overrides are set in the individual Helix tags. Refer to the MakeBundle mover for options that both movers have in common. Additional options include:

[parameter]_min, [parameter]_max: Minimum and maximum parameter values for a range to be sampled.
[parameter]_samples: The number of samples. Note that the total number of samples is the product of all individual samples, and this can get quite large very fast.
[parameter]_copies_helix: This option may only be specified in a Helix sub-tag. It indicates that a particular parameter for that helix is always set to the same value as that parameter from a previously-defined helix. See below for an example.
max_samples: The maximum number of samples permitted. If the total number of samples is larger than this, the mover throws an error at apply time. This is meant as a protection for the user, to prevent unreasonably large grid sampling jobs from being attempted. The default value of 10,000 samples is conservative, and may be increased.
scorefxn: The scoring function to use. This must be specified, since this mover selects the lowest-energy bundle generated.
selection_type: Although the lowest-energy bundle is selected by default ("low"), the user may optionally specify that the highest-energy bundle ("high") be selected instead.
pre_selection_mover: If specified, this mover will be applied to each generated bundle prior to energy evaluation. This can be useful for side-chain packing or minimization as backbone conformations are sampled. Note that this can greatly increase runtime, however. Note also that, if a mover is used that alters the backbone conformation, the conformation may no longer lie within the Crick parameter space.
dump_pdbs: If true, a PDB file is written for every bundle conformation sampled. False by default.
pdb_prefix: The prefix for the PDB filenames if PDB files are being written. Filenames will be of the format [prefix]_#####.pdb. This defaults to "bgs_out".

Note that default parameter ranges are applied separately to each helix. For example, the following script would perform 16 samples (4 each for r0 of helix 1 and r0 of helix 2):

<BundleGridSampler name="bgs1" helix_length=20 scorefxn="sfxn1" r0_min=5.0 r0_max=8.0 r0_samples=4 omega0=0.05 delta_omega0=0 delta_omega1=0 delta_t=0>
     <Helix />
     <Helix delta_omega0=3.14 />
</BundleGridSampler>

In order to sample a range of parameters, keeping a parameter value for two different helices the same, the [parameter]_copies_helix option may be used in a Helix tag. The helix to be copied must be declared before the helix that has the [parameter]_copies_helix option. The following script, for example, carries out 4 samples, with r0 for both helices ranging from 5 to 8 (and always the same for both helices):

<BundleGridSampler name="bgs1" helix_length=20 scorefxn="sfxn1" r0_min=5.0 r0_max=8.0 r0_samples=4 omega0=0.05 delta_omega0=0 delta_omega1=0 delta_t=0>
     <Helix />
     <Helix delta_omega0=3.14 r0_copies_helix=1/>
</BundleGridSampler>

BundleGridSampler

BundleGridSampler

Description

See also