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density-fitness

Section: User Commands (1)
Updated: 2020-11-23
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NAME

density-fitness - Calculates per-residue electron density scores real-space R, real-space correlation coefficient, EDIAm, and OPIA

SYNOPSIS

density-fitness [OPTION] <mtz-file> <coordinates-file> [output]

density-fitness [OPTION] --hklin=<mtz-file> --xyzin=<coordinates-file> [--output=<output>]

density-fitness [OPTION] --fomap=<fo-map-file> --dfmap=<df-map-file> --reslo=<low-resolution> --reshi=<high-resolution> --xyzin=<input [--output=<output>]

DESCRIPTION

The program density-fitness calculates electron density metrics, for main- (includes Cβ atom) and side-chain atoms of individual residues.

For this calculation, the program uses the structure model in either PDB or mmCIF format and the electron density from the 2mFo-DFc and mFo-DFc maps. If these maps are not readily available, the MTZ file and model can be used to calculate maps clipper. Density-fitness support both X-ray and electron diffraction data.

This program is essentially a reimplementation of edstats, a program available from the CCP4 suite. However, the output now contains only the RSR, SRSR and RSCC fields as in edstats with the addition of EDIAm and OPIA and no longer requires pre-calculated map coefficients.

The real-space R factor (RSR) is defined (Brändén & Jones, 1990; Jones et al., 1991) as:: RSR = Σ |ρobs - ρcalc| / Σ |ρobs + ρcalc|

The SRSR is the estimated sigma for RSR.

The real-space correlation coefficient (RSCC) is defined as:

RSCC = cov(ρobs,ρcalc) / sqrt(var(ρobs) var(ρcalc))

where cov(.,.) and var(.) are the sample covariance and variance (i.e. calculated with respect to the sample means of ρobs and ρcalc).

The EDIAm score is a per-residue score based on the atomic EDIA value and the OPIA score gives the percentage of atoms in the residue with EDIA score is above 0.8.

OPTIONS

When using MTZ files, the input and output files do not need the option flag. If no output file is given, the result is printed to stdout.

When using map files, the resolution must be specified using the reshi and reslo options.

--xyzin: The coordinates file in either PDB or mmCIF format. This file may be compressed with gzip. --fomap and --dfmap The 2mFo-DFc and mFo-DFc map files respectively. Both are required and if these are specified, the resolution must also be specified.
--reslo and --reshi: The low and high resolution for the specified map files.
--hklin: The MTZ file. If this option is specified, the maps will be calculated using the information in this file.
--sampling-rate: The sampling rate to use when creating maps. Default is 1.5.
--recalc: By default the maps are read from the MTZ file, but you can also opt to recalculate the maps, e.g. when the structure no longer corresponds to the structure used to calculate the maps in the MTZ file.
--aniso-scaling: Accepted values for this option are observed and calculated or none. Used when recalculating maps.
--no-bulk: When specified, a bulk solvent mask is not used in recalculating the maps.
--components (or --compounds): Specify the path of the CCD file components.cif. By default the one installed by libcifpp is used, use this option to override this default.
--extra-compounds: A file containing information for residues in this specific target. This file may be in either CCD or CCP4 monomer library format.
--mmcif-dictionary: Specify the path to the mmcif pdbx dictionary file. The default is to use the dictionary installed by libcifpp, use this option to override this default.
--no-validate: Omit the validation of the input mmCIF file. This will force output even in case the input file contains errors.
--electron-scattering: Use electron scattering factors instead of X-ray scattering factors.
--use-auth-ids: By default, when reading mmCIF files, the label_xxx_id is used in the edstats output. Use this flag to force output with the auth_xxx_ids.
--output-format: By default a JSON file is written, unless the filename ends with .eds. Use this option to force output in edstats or json format.
--verbose,-V: Be more verbose, useful to diagnose validation errors.

REFERENCES

References:

Statistical quality indicators for electron-density maps: Tickle, I. J. (2012). Acta Cryst. D68, 454-467. DOI: 10.1107/S0907444911035918
Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures: Agnes Meyder, Eva Nittinger, Gudrun Lange, Robert Klein, and Matthias Rarey Journal of Chemical Information and Modeling 2017 57 (10), 2437-2447 DOI: 10.1021/acs.jcim.7b00391

AUTHOR

Written by Maarten L. Hekkelman <maarten@hekkelman.com>

REPORTING BUGS

Report bugs at https://github.com/PDB-REDO/density-fitness/issues

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Time: 14:15:38 GMT, August 31, 2021