pegi3s/pdb-tools repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of PDB-tools⁠, a swiss army knife for manipulating and editing PDB files.

⁠Using the PDB-tools image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/pdb-tools bash -c <pdb-tool>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <pdb-tool> to the name of the PDB-tool you want to use.

For instance, in order to download the 1BRS PDB structure, you should run: docker run --rm -v /your/data/dir:/data pegi3s/pdb-tools bash -c "pdb_fetch 1brs > 1brs.pdb"

⁠Using the PDB-tools image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/pdb-tools bash -c <pdb-tool>