Back to SimpleMetrics page.

PerResidueRMSDMetric

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

Autogenerated Tag Syntax Documentation:


Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) This is the RMSD for each residue between the input and the set comparison pose. If native is set on the cmd-line and use_native is true, we will use that. Default is to calculate all_heavy atoms - but this can be set . Make sure that reference pose and set pose are the same length . We match all corresponding atoms for each residue to match. By default we do not fail and are robust - only matching what we can for each residue.

<PerResidueRMSDMetric name="(&string;)" custom_type="(&string;)"
        output_as_pdb_nums="(&string;)" residue_selector="(&string;)"
        residue_selector_ref="(&string;)" robust="(true &bool;)"
        use_native="(false &bool;)" super="(false &bool;)"
        rmsd_type="(&rmsd_types;)" desymmetrize_selector="(true &bool;)" />
  • 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.
  • output_as_pdb_nums: If outputting to scorefile use PDB numbering instead of Rosetta (default)
  • residue_selector: If a residue selector is present, we only calculate and output metrics for the subset of residues selected.
  • 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.
  • robust: Set whether we are robust to atom mismatches for selected residues. By default we only match atoms that are corresponding. (True).
  • use_native: Use the native if present on the cmd-line.
  • super: Run a superposition on the residues in the residue_selector (or all) before RMSD calculation and the atoms slected for RMSD
  • rmsd_type: Type of calculation. Current choices are: [rmsd_all, rmsd_all_heavy, rmsd_protein_bb_ca, rmsd_protein_bb_heavy, rmsd_protein_bb_heavy_including_O, rmsd_sc, rmsd_sc_heavy]
  • desymmetrize_selector: Should we desymmetrize the residue selector if we have a symmetric pose?

See Also