scripting_documentation/RosettaScripts/xsd/mover_DnaInterfacePacker

Autogenerated Tag Syntax Documentation:

Intended to perform anything one would want to do in a DNA interface that uses a single incarnation of the RotamerSets/InteractionGraph combo. For basic packing/designing, the more basic PackRotamersMover can be used instead, provided it receives the appropriate TaskFactory/TaskOperations. This derived class, however, takes advantage of the reusability of packer data to accomplish some higher-level functions, such as rapid estimations of multi-state specificity, reversions, and mutational scanning.

<DnaInterfacePacker name="(&string;)" binding="(&bool;)" base_only="(&bool;)"
        minimize="(&bool;)" reversion_scan="(&bool;)"
        probe_specificity="(&non_negative_integer;)" pdb_output="(&bool;)"
        protein_scan="(&bool;)" allowed_types="(&bool;)" scorefxn="(&string;)"
        task_operations="(&task_operation_comma_separated_list;)"
        packer_palette="(&named_packer_palette;)" />

binding: calculate binding energy
base_only: consider only interaction with the DNA bases
minimize: minimize protein side chains at the interface
reversion_scan: revert mutations that do not contribute to the specificity score
probe_specificity: calculate binding energy of designed protein for alternative DNA targets and calculate a specificity score
pdb_output: write out unbound pose to verify proper interface separation
protein_scan: brief runs a single-residue scan of user-defined amino acid possibilities to estimate affinity and specificity of single mutants w/ respect to relevant DNA
allowed_types: allowed residue types for design. default: ACDEFGHIKLMNPQRSTVWY;
scorefxn: Name of score function to use
task_operations: A comma-separated list of TaskOperations to use.
packer_palette: A previously-defined PackerPalette to use, which specifies the set of residue types with which to design (to be pruned with TaskOperations).

scripting_documentation/RosettaScripts/xsd/mover_DnaInterfacePacker_type