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

version 1.0.1                                      2020-11-23                                 density-fitness(1)