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CDRDihedralConstraintMover

Author

Part of the RosettaAntibody and RosettaAntibodyDesign (RAbD) Framework

Purpose

Adds Circular Harmonic Dihedral Constraints to the Phi and Psi dihedral angles to a particular CDR either using the current computed North/Dunbrack CDR Cluster (requires AHo numbered antibody) or general constraints. These constraints keep the CDR structure from moving too much during backbone optimization such as FastRelax. Please see the constraints page for more information on constraints and this page for more information on antibody numbering.

<CDRDihedralConstraintMover name="dih_mover" cdr="(&string (ex: L1))" use_cluster_csts="(&bool)" />

Required

• cdr (& string): CDR to add the constraints to (ex: H1 or h1)

Optional

Cluster-based Constraint Settings

• use_cluster_csts (&bool) (Default=true): Add cluster-based constraints? If false, we will use general dihedral constraints.

• force_cluster (&string) (Ex: L1-11-1): Force addition of cluster constraints of this particular cluster. Must be same CDR length as the current CDR.

• cluster_data_required (&size) (Default=10): Value for cluster-based dihedral csts -> general dihedral csts switch. If number of total structures used for cluster-based constraints is less than this value, general dihedral constraints will be used. More data = better predictability.

• use_general_constraints_on_failure (&bool) (Default=true): Add general constraints if cluster-based constraint addition failed. It can fail if the cluster cannot be determined (such as some H3 loops), or if there is not enough data (see cluster_data_required option. If this is false and cluster-based constraint addition failed, then we will not do anything.

• use_outliers (&bool) (Default=false): Use a separate set of data for cluster-based constraints which contained outliers for the calculation. Outliers are defined as having a dihedral distance of > 40 degrees and an RMSD of >1.5 A to the cluster center. Use to increase sampling of small or rare clusters.

General Constraint Settings

• general_phi_sd (&real) (Default=16): Standard deviation to use for phi while using general dihedral circular harmonic constraints
• general_psi_sd (&real) (Default=16): Standard deviation to use for psi while using general dihedral circular harmonic constraints