Page created by Vikram K. Mulligan (vmulligan@flatironinstitute.org). Last modified 12 October 2018. Back to Mover page.
Generates a helical bundle using the Crick equations (which describe a helix of helices) or modified Crick equations (describing a laterally-squashed helix of helices). This mover is general enough to create arbitrary helices using arbitrary backbones. Since strands are a special case of a helix (in which the turn per residue is about 180 degrees), the mover can also generate beta-barrels or other strand bundles. The generated secondary structure elements are disconnected, so subsequent movers (e.g. GeneralizedKIC) must be invoked to connect them with loops. Parameters are stored with the pose, and are written in REMARK lines on PDB output.
Helix types are defined with crick_params files, located in the Rosetta database in database/protocol_data/crick_parameters (or provided by the user). Support for Crick parameter files defining helices in which the repeating unit is more than one residue has recently been added. For more information on this file type, see this page.
Autogenerated Tag Syntax Documentation:
The MakeBundle mover builds a helical bundle parametrically, using the Crick parameterization, given a set of Crick parameter values. Note that the Crick parameterization is compatible with arbitrary helices (including strands, which are special cases of helices in which the turn per residue is about 180 degrees).
References and author information for the MakeBundle mover:
MakeBundle Mover's author(s): Vikram K. Mulligan, Systems Biology, Center for Computational Biology, Flatiron Institute [vmulligan@flatironinstitute.org]
<MakeBundle name="(&string;)" r0="(0.000000 ℜ)" omega0="(0.000000 ℜ)"
delta_omega0="(0.000000 ℜ)" delta_omega1="(0.000000 ℜ)"
delta_t="(0.000000 ℜ)" z0_offset="(0.000000 ℜ)"
z1_offset="(0.000000 ℜ)" epsilon="(1.000000 ℜ)"
repeating_unit_offset="(0 &non_negative_integer;)"
r1_peratom="(0 &real_wsslist;)" omega1="(0.000000 ℜ)"
z1="(0.000000 ℜ)" 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;)" use_degrees="(false &bool;)"
symmetry="(0 &non_negative_integer;)"
symmetry_copies="(0 &non_negative_integer;)" reset="(false &bool;)"
crick_params_file="(&string;)" residue_name="(&string;)"
helix_length="(0 &non_negative_integer;)" >
<Helix crick_params_file="(&string;)" residue_name="(&string;)"
helix_length="(0 &non_negative_integer;)" r0="(0.000000 ℜ)"
r0_copies_helix="(0 &non_negative_integer;)" omega0="(0.000000 ℜ)"
omega0_copies_helix="(0 &non_negative_integer;)"
pitch_from_helix="(0 &non_negative_integer;)"
delta_omega0="(0.000000 ℜ)"
delta_omega0_copies_helix="(0 &non_negative_integer;)"
delta_omega1="(0.000000 ℜ)"
delta_omega1_copies_helix="(0 &non_negative_integer;)"
delta_t="(0.000000 ℜ)"
delta_t_copies_helix="(0 &non_negative_integer;)"
z0_offset="(0.000000 ℜ)"
z0_offset_copies_helix="(0 &non_negative_integer;)"
z1_offset="(0.000000 ℜ)"
z1_offset_copies_helix="(0 &non_negative_integer;)"
epsilon="(1.000000 ℜ)"
epsilon_copies_helix="(0 &non_negative_integer;)"
repeating_unit_offset="(0 &non_negative_integer;)"
r1_peratom="(0 &real_wsslist;)" omega1="(0.000000 ℜ)"
omega1_copies_helix="(0 &non_negative_integer;)" z1="(0.000000 ℜ)"
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;)" />
</MakeBundle>
Subtag Helix:
The Rosetta database currently contains several sets of minor helix parameters:
This script generates an antiparallel beta-barrel with a bundle of alpha-helices on the inside.
<MakeBundle name="bundle1" set_bondlengths="true" set_bondangles="true" residue_name="ALA" crick_params_file="beta_strand" symmetry="16" r0="29" omega0="0.075" helix_length="20" >
#The parameters set above ensure that by default, each "helix" will actually be a strand:
<Helix /> #A strand
<Helix delta_omega0="0.19634954" invert="1" delta_t="0.25" delta_omega1="1.5707963" /> #An offset, inverted strand.
<Helix r0="21" omega0="0.05" crick_params_file="alpha_helix" helix_length="40" /> #An alpha-helix.
#The three elements defined above are repeated 16 times about the bundle axis to make the bundle.
</MakeBundle>
Note that RosettaScripts requires some sort of input on which to operate, but this mover, by default, deletes input geometry and replaces it with the generated geometry. When running RosettaScripts, one can either pass in a dummy PDB file with the -in:file:s flag, or a dummy FASTA file with the -in:file:fasta flag.