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RMSDMetric

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Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) This metric calculates the RMSD between the input and the set comparison pose. You may use the cmd-line native if the option use_native is true. Default is to calculate all_heavy atoms - but this can be set using the option rmsd_types.

We match all corresponding atoms for each residue to match. By default we do not fail and are robust to length mismatches - only matching what we can for each residue.

<RMSDMetric name="(&string;)" custom_type="(&string;)"
        reference_name="(&string;)" residue_selector="(&string;)"
        residue_selector_ref="(&string;)" robust="(true &bool;)"
        use_native="(false &bool;)" super="(false &bool;)"
        rmsd_type="(&rmsd_types;)" />
  • 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.
  • 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.
  • 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 selected 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]

See Also