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PerResidueDensityFitMetric

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:

Authors: Jared Adolf-Bryfogle (jadolfbr@gmail.com) and Frank Dimaio (fdimaio@gmail.com) Calculate either a correlation (match_res true) or zscore related to the fit to the density. Uses internal density tools to do so. Numbers and cutoffs match well with Coot's density fit analysis tool. Zscore uses weighted sum of density, density-compared-to-neighbors, rama (where applicable) and cart_bonded to compute) Correlation is same values used to calculate density scores. Zscore reference is here: eLife 2016, Dimaio

<PerResidueDensityFitMetric name="(&string;)" custom_type="(&string;)"
        output_as_pdb_nums="(false &bool;)" residue_selector="(&string;)"
        sliding_window_size="(3 &positive_integer;)" match_res="(false &bool;)"
        mixed_sliding_window="(false &bool;)"
        use_selector_as_zscore_mask="(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+chain instead of Rosetta (1 - N numbering)
  • residue_selector: If a residue selector is present, we only calculate and output metrics for the subset of residues selected. 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.
  • sliding_window_size: Sliding window size for density calculation
  • match_res: Use density correlation instead of a zscore to fit to density
  • mixed_sliding_window: Use a window size of 3 for protein and 1 for glycans. May skew results.
  • use_selector_as_zscore_mask: Use the selector as true mask to calculate the Zscore. Otherwise, use it just as a selection for computation. Default true.

See Also