Autogenerated Tag Syntax Documentation:
Note: The LayerDesign TaskOperation will likely be deprecated at some point in the future in favour of the LayerSelector ResidueSelector. It is strongly recommended that users start to switch over to the LayerSelector ResidueSelector, which permits greater flexibility in selecting residues. Design residues with selected amino acids depending on the enviroment--accessible surface area. The layer of each residue is assigned to one of the three basic layers--core, boundary or surface-- depending on the accessible surface area of mainchain + CB, or depending on the number of neighbours in a cone extending along the CA-CB vector --if the use_sidechain_neighbors option is used.
<LayerDesign name="(&string;)" use_original_non_designed_layer="(true &bool;)"
layer="(core_boundary_surface_Nterm_Cterm &string;)"
repack_non_design="(true &bool;)" ignore_pikaa_natro="(false &bool;)"
use_sidechain_neighbors="(&bool;)" sc_neighbor_dist_midpoint="(ℜ)"
sc_neighbor_denominator="(ℜ)"
sc_neighbor_angle_shift_factor="(ℜ)"
sc_neighbor_angle_exponent="(ℜ)"
sc_neighbor_dist_exponent="(ℜ)" pore_radius="(ℜ)"
core="(ℜ)" surface="(ℜ)" core_E="(ℜ)" core_L="(ℜ)"
core_H="(ℜ)" surface_E="(ℜ)" surface_L="(ℜ)"
surface_H="(ℜ)" make_rasmol_script="(&bool;)"
blueprint="(&string;)" use_symmetry="(true &bool;)"
verbose="(false &bool;)" restrict_restypes="(true &bool;)"
make_pymol_script="(false &bool;)" >
<core >
<all copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Helix copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixCapping copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixStart copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Loop copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Strand copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
</core>
<boundary >
<all copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Helix copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixCapping copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixStart copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Loop copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Strand copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
</boundary>
<surface >
<all copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Helix copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixCapping copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixStart copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Loop copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Strand copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
</surface>
<Nterm >
<all copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Helix copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixCapping copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixStart copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Loop copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Strand copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
</Nterm>
<Cterm >
<all copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Helix copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixCapping copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixStart copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Loop copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Strand copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
</Cterm>
<CombinedTasks name="(&string;)" >
<all copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Helix copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixCapping copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixStart copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Loop copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Strand copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<TaskOperation Tag ... />
</CombinedTasks>
<TaskLayer >
<TaskOperation Tag ... />
<all copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Helix copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixCapping copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<HelixStart copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Loop copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
<Strand copy_layer="(&string;)" aa="(&string;)" append="(&string;)"
exclude="(&string;)" operation="(&layer_design_operation_behavior;)"
specification="(&layer_design_specification_behavior;)" />
</TaskLayer>
</LayerDesign>
Subtag core: XRW TO DO
Subtag all: XRW TO DO
Subtag Helix: XRW TO DO
Subtag HelixCapping: XRW TO DO
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"TaskOperation Tag": Any of the RosettaScripts TaskOperation tags
Subtag TaskLayer: XRW TO DO
"TaskOperation Tag": Any of the RosettaScripts TaskOperation tags
Subtag all: XRW TO DO
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