density-fitness - Calculates per-residue electron density scores
real-space R, real-space correlation coefficient, EDIAm, and OPIA
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>]
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.
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.
- 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.
Written by Maarten L. Hekkelman <maarten@hekkelman.com>
Report bugs at
https://github.com/PDB-REDO/density-fitness/issues