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RMSDMetric

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) 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.

References and author information for the RMSDMetric simple metric:

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

<RMSDMetric name="(&string;)" custom_type="(&string;)"
        reference_name="(&string;)" residue_selector="(&string;)"
        residue_selector_ref="(&string;)" residue_selector_super="(&string;)"
        residue_selector_super_ref="(&string;)" robust="(true &bool;)"
        use_native="(false &bool;)" super="(false &bool;)"
        cyclic="(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. 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: Optional 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.
  • residue_selector_super: Optional selector for superposition. If not given will use residue_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.
  • residue_selector_super_ref: Optional selector for superposition of 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.
  • 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
  • cyclic: if the pose is cyclic, this will compute RMSDs on all equivalent matches and return the smallest 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