recipe biobb_structure_checking

BioBB_structure_checking performs MDWeb structure checking set as a command line utility.



APACHE / Apache Software License



Biobb_structure_checking performs a checking of the quality of a 3D structure intended to facilitate the setup of molecular dynamics simulation of protein or nucleic acids systems. Biobb_structure_checking package allows to configure the system (selection of model/chains,alternative location, addition of disulfide bonds and hydrogen atoms, side chain mutations), to detect and fix structure errors (missing side chain atoms, backbone breaks, amide assignments, incorrect chirality). It works with structures obtained from the Protein Data Bank or user provided. The Biobb_structure_checking package provides a command line utility ( and a python API ( The latest documentation of this package can be found in our readthedocs site:

package biobb_structure_checking

(downloads) docker_biobb_structure_checking



depends biopython:


depends numpy:

depends pip:

depends psutil:

depends python:


depends setuptools:



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 biobb_structure_checking

and update with::

   mamba update biobb_structure_checking

To create a new environment, run:

mamba create --name myenvname biobb_structure_checking

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<tag>

(see `biobb_structure_checking/tags`_ for valid values for ``<tag>``)

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