scripting_documentation/RosettaScripts/xsd/rs_DensityFitResidueSelector

Autogenerated Tag Syntax Documentation:

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) and Sebastian Raemish (raemish@scripps.edu). Select residues that have a good electron density fit. (Or bad fit using the invert option). 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: eLife 2016, Dimaio TIPS: In order to do native comparisons, run the PerResidueDensityFit on the input (top of RS), and then use this selector on that.

<DensityFitResidueSelector name="(&string;)" invert="(false &bool;)"
        cutoff="(-.5 &real;)" sliding_window_size="(3 &positive_integer;)"
        mixed_sliding_window="(false &bool;)" match_res="(false &bool;)"
        use_selector_as_zscore_mask="(true &bool;)" den_fit_metric="(&string;)"
        use_cache="(false &bool;)" prefix="(&string;)" suffix="(&string;)"
        fail_on_missing_cache="(false &bool;)" residue_selector="(&string;)" />

invert: Select residues that have a bad density fit instead of those with good density fit.
cutoff: Cutoff of bad match to density
sliding_window_size: Sliding window size for density calculation
mixed_sliding_window: Use a window size of 3 for protein and 1 for glycans. May skew results.
match_res: Use density correlation instead of a zscore to fit to density
use_selector_as_zscore_mask: Use the selector as true mask to calculate the Zscore. Otherwise, use it just as a selection for result. Default true.
den_fit_metric: Use a previously defined Per-Residue Density Fit Metric (use for caching data
use_cache: Use any cached SM data instead of recaclulating. Data can be cached by calling RunSimpleMetrics on the metric before using this residue selector. The metric will need to be defined before this selector, perhaps in another section of SIMPLE_METRICS.
prefix: Prefix for the cached data.
suffix: Suffix for the cached data.
fail_on_missing_cache: If we are using cached data, should we fail on no cache?
residue_selector: A Residue selector mask. Used to only compute Zscore among a set of residues. Useful for protein vs glycan density. Since match_res is NOT a zscore, the selector acts as an AND selector, so we only compute the correlations on this set. . 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.

scripting_documentation/RosettaScripts/xsd/rs_DensityFitResidueSelector_type