recipe density-fitness

Application to calculate the density statistics (RSR, SRSR, RSCCS, EDIAm and OPIA) for x-ray structures

Homepage:

https://github.com/PDB-REDO/density-fitness

Documentation:

https://github.com/PDB-REDO/density-fitness/blob/v1.2.0/doc/density-fitness.pdf

License:

BSD / BSD-2-Clause

Recipe:

/density-fitness/meta.yaml

Links:

doi: 10.1107/S0907444911035918, doi: 10.1021/acs.jcim.7b00391

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.

package density-fitness

versions:

1.2.0-0

depends libcifpp:

>=9.0.5,<10.0a0

depends libgcc:

>=13

depends libpdb-redo:

>=3.3.1,<4.0a0

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

requirements:

additional platforms:

linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install density-fitness

and update with::

   mamba update density-fitness

To create a new environment, run:

mamba create --name myenvname density-fitness

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/density-fitness:<tag>

(see `density-fitness/tags`_ for valid values for ``<tag>``)

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