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DihedralDistanceMetric

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com)

Reference

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design Jared Adolf-Bryfogle, J. W Labonte, J. C Kraft, M. Shapavolov, S. Raemisch, T. Lutteke, F. Dimaio, C. D Bahl, J. Pallesen, N. P King, J. J Gray, D. W Kulp, W. R Schief bioRxiv 2021.09.27.462000; https://doi.org/10.1101/2021.09.27.462000

Autogenerated Tag Syntax Documentation:

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) Calculate DihedralDistance metric. This is the normalized metric in degrees Works on protein and carbohydrate backbones

Metric described in: North B, Lehmann A, Dunbrack RL. A new clustering of antibody CDR loop conformations. J Mol Biol 2011;406:228-256.

References and author information for the DihedralDistanceMetric simple metric:

DihedralDistanceMetric SimpleMetric's author(s): Jared Adolf-Bryfogle, Scripps Research Institute [jadolfbr@gmail.com]

<DihedralDistanceMetric name="(&string;)" custom_type="(&string;)"
        include_omega="(false &bool;)" use_native="(false &bool;)"
        reference_name="(&string;)" residue_selector="(&string;)"
        residue_selector_ref="(&string;)" />
  • custom_type: Allows multiple configured SimpleMetrics of a single type to be called in a single RunSimpleMetrics and SimpleMetricFeatures. The custom_type name will be added to the data tag in the scorefile or features database.
  • include_omega: Do we include protein omega in calculations? Default false.
  • use_native: Use the native if present on the cmd-line.
  • reference_name: Name of reference pose to use (Use the SavePoseMover to create a reference pose)
  • residue_selector: Calculate the RMSD for these residues for both reference and main pose. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.
  • residue_selector_ref: Selector for the reference pose (input native or passed reference pose. ). Residues selected must be same number of residues selected for the main selector. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.

See Also