density-fitness

This is the repository for density-fitness, an application to calculate density statisctics. This program is part of the PDB-REDO suite of programs.

Installation

The easiest way to build and install density-fitness is by using the builder script, this is a CMake file that will build all missing dependencies automatically. Use it like this:

git clone https://github.com/PDB-REDO/density-fitness.git -b density-fitness-builder
cd density-fitness
cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$HOME/.local
cmake --build build
cmake --install build

Those commands will create an executable and install it in $HOME/.local. You can specify any other path here of course.

Please note that density-fitness built this way still requires a CCD components.cif file. This file should be located in '/usr/share/libcifpp/' or '/var/cache/libcifpp/'. You can of course also provide your own version of this file using the command line argumentsn (See options below).

If you want to install the classic way, you have to install all dependencies first. See the documentation for libpdb-redo on installing all prerequisites.

After that, density-fitness can be built as follows:

git clone https://github.com/PDB-REDO/density-fitness.git
cd density-fitness
mkdir build
cd build
cmake ..
cmake --build .
cmake --install .

When building on Windows you should replace cmake --build . with cmake --build . --config Release.

This checks out the source code from github, creates a new directory where cmake stores its files. Run a configure, build the code and run tests. And then it installs the library and auxiliary files.

The default is to install everything in $HOME/.local on Linux and %LOCALAPPDATA% on Windows (the AppData/Local folder in your home directory). You can change this by specifying the prefix with the CMAKE_INSTALL_PREFIX variable.

Usage

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