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

(downloads) docker_density-fitness

Versions:

1.2.0-0

Depends:

  • on libcifpp >=9.0.5,<10.0a0

  • on libgcc >=13

  • on libpdb-redo >=3.3.1,<4.0a0

  • on libstdcxx >=13

  • on libzlib >=1.3.1,<2.0a0

Additional platforms:
linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install density-fitness

to add into an existing workspace instead, run:

pixi add density-fitness

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install density-fitness

Alternatively, to install into a new environment, run:

conda create -n envname density-fitness

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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