InitializeFromCommandline

Reads commandline options. For example, -ex1 -ex2. This taskoperation will complain about an unimplemented method, but you can safely ignore the message.

IncludeCurrent

Includes current rotamers (eg - from input pdb) in the rotamer set. These rotamers will be lost after a packing run, so they are only effective upon initial loading of a pdb!

LayerDesign

Design residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface area of mainchain + CB. If resfile is read before calling this operation, this operation is not applied for the residues defined by PIKAA.

Selected amino acid types for each layer:

• Core
• Loop: AFILPVWY
• Strand: FIL VWY
• Helix: AFIL VWY ( P only at the beginning of helix )
• Boundary
• Loop: ADEGIKLNPQRSTVY
• Strand: DE IKLN QRSTVY
• Helix: ADE IKLN QRSTVY ( P only at the beginning of helix )
• HelixCapping: DNST
• Surface
• Loop: DEGHKNPQRST
• Strand: DE HKN QRST
• Helix: DE HKN QRST ( P only at the beginning of helix )
• HelixCapping: DNST

Option list

• layer ( default "core_boundary_surface" ) : layer to be designed, other ex. core_surface means only design core and surface layer
• use_original_non_designed_layer ( default, 0 ) : use original sequence for non designed layers, otherwise the residues on the layers turned into Ala
• pore_radius ( default 2.0) : pore radius for calculating accessible surface area
• burial ( default 20.0) : residues of which asa is < burial are defined as burial
• surface ( default 40.0) : residues of which asa is > surface are defined as surface

LimitAromaChi2Operation

Prevent to use the rotamers of PHE, TYR and HIS that have chi2 far from 90.

• chi2max ( default 110.0 ) : max value of chi2 to be used
• chi2min ( default 70.0 ): min value of chi2 to be used

NoRepackDisulfides

Do not allow disulfides to repack.

ReadResfile

Read a resfile on the commandline. Specifying this operation but not supplying a resfile will cause a crash. filename=(&string)

RestrictToRepacking

Only allow residues to repack. No design.

RestrictResidueToRepacking

Restrict a single residue to repacking. No design. resnum=(0&integer)

RotamerExplosion

Sample residue chi angles much more finely during packing.

PreventRepacking

Do not allow repacking at all. Freezes residues. resnum=(0&int)

RestrictToInterface

Restricts to interface between two protein chains along a specified jump and with a given radius. rb_jump=(&integer, 1) distance=(&Real, 8.0)

RestrictToInterfaceVector

Restricts the task to residues defined as interface by the InterfaceVectorDefinitionCalculator

  <RestrictToInterfaceVector name=(& string) chain1_num=1 chain2_num=2 CB_dist_cutoff=10.0 nearby_atom_cutoff=5.5 vector_angle_cutoff=75.0 vector_dist_cutoff=9.0/>

ProteinInterfaceDesign

Restricts to the task that is the basis for protein-interface design.

• repack_chain1=(1, &bool)
• repack_chain2=(1, &bool)
• design_chain1=(0, &bool)
• design_chain2=(1, &bool)
• allow_all_aas=(0 &bool)
• design_all_aas=(0 &bool)
• interface_distance_cutoff=(8.0, &Real)
• jump=(1&integer) chains below, and above the jump are called chain1 and chain2 above.

DetectProteinLigandInterface

Setup packer task based on the detect design interface settings from enzyme design.

<DetectProteinLigandInterface name=(&string) cut1=(6.0 &Real) cut2=(8.0 &Real) cut3=(10.0 &Real) cut4=(12.0 &Real) design=(1 &bool) resfile=("" &string)/>

The task will set to design all residues with a Calpha within cut1 of the ligand (specifically the last ligand), or within cut2 of the ligand, where the Calpha-Cbeta vector points toward the ligand. Those residues within cut3 or within cut4 pointing toward the ligand will be set to repack. All others will be set to be fixed. Setting design to false will override the design (cut1/cut2) settings.

If resfile is specified, the listed resfile will be read in the settings therein applied to the task. Any positions set to "AUTO" (and only those set to AUTO) will be subjected the detect design interface procedure as described above.

ProteinLigandInterfaceUpweighter

Specifically upweight the strength of the protein-ligand interaction energies by a given factor.

<ProteinLigandInterfaceUpweighter name=(&string) lig_packer_weight=(1.0 &Real)/>

OperateOnCertainResidues

Allows specification of Residue Level Task Operations based on residue properties specified with ResFilters.

Example:

<OperateOnCertainResidues name=PROTEINnopack>
  <PreventRepackingRLT/> //Only one Residue level task per OperateOnCertainResidues block
  <ResidueHasProperty property=PROTEIN/>
</OperateOnCertainResidues>

RestrictAbsentCanonicalAAS

Restrict design to user-specified residues. resnum=(0 &integer) keep_aas=(string). if resnum is left as 0, the restriction will apply throughout the pose. For instance, to generate an ala-pose:

resnum=0 keep_aas="A"

and call PackRotamersMover

ThreadSequence

Threads a fasta-formatted sequence onto the source pdb. target_sequence=(&string)

and call PackRotamersMover

InitializeExtraRotsFromCommandline

Under development and untested. Use at your own risk.

SetRotamerCouplings

Under development and untested. Use at your own risk.

AppendRotamer

Under development and untested. Use at your own risk.

AppendRotamerSet

Under development and untested. Use at your own risk.

PreserveCBeta

Under development and untested. Use at your own risk.

SetSurfaceScoreWeight

Under development and untested. Use at your own risk.

RestrictYSDesign

Restrict amino acid choices during design to Tyr and Ser. This is similar to the restricted YS alphabet used by Sidhu's group during in vitro evolution experiments. Under development and untested. Use at your own risk.

Residue Level TaskOperations

Use these as a subtag for special OperateOnCertainResidues TaskOperation. Only one may be used per OperateOnCertainResidues

RestrictToRepackingRLT

PreventRepackingRLT

AddBehaviorRLT

RestrictAbsentCanonicalAASRLT*

RotamerExplosion

ResFilters

Use these as a subtag for special OperateOnCertainResidues TaskOperation. Only one may be used per OperateOnCertainResidues

ResidueHasProperty

settings:

• property. e.g. DNA, PROTEIN, POLAR, CHARGED (one only)

ResidueLacksProperty

ChainIs

Selects a set of residues based on their chain letter in the original PDB.

• chain: defaults to "A"

ChainIsnt

Excludes a set of residues based on their chain letter in the original PDB.

• chain: defaults to "A"

ResidueName3Is

• name3: eg arg,lys,gua (one only)

ResidueName3Isnt

ResidueIndexIs

• indices

comma-separated list of rosetta residue indices (1 to nres) e.g. indices=1,2,3,4,33

ResidueIndexIsnt

ResiduePDBIndexIs

• indices: comma-separated list of chain.pos identifiers e.g. indices=A.2,C.100,D.-10

ResiduePDBIndexIsnt