Downloading the PDB-REDO software

If you are working with sensistive data you can install PDB-REDO locally on Linux and WSL. You can also use it to run large sets of custom PDB-REDO jobs. Alternatively, you can use the PDB-REDO API to commit batches of custom calculations.

Downloading PDB-REDO entries

You can download PDB-REDO entries using you favorite molecular graphics program or manually. You can also download the entire databank at once. Below are some basic examples, more data from the PDB-REDO databank is described underneath.

Molecular graphics:

• YASARA has a native PDB-REDO interface to show models.
• CCP4mg can download PDB-REDO models and maps.
• (Win)COOT also has a native PDB-REDO interface that shows models and maps. When available anomalous maps are also shown.
• Moorhen can also show models and maps directly from the PDB-REDO databank.

Manual download (single entries) via the website or using wget:

• wget https://pdb-redo.eu/db/9xyz/9xyz_final.cif downloads the fully optimised (re-refined and rebuilt) coordinate file.
• wget https://pdb-redo.eu/db/9xyz/9xyz_final.mtz downloads the MTZ files to generate electron density maps.
• wget https://pdb-redo.eu/db/9xyz/zipped downloads all files of a PDB-REDO entry.

Download entire PDB-REDO databank using rsync:

• rsync -av --exclude=attic rsync://rsync.pdb-redo.eu/pdb-redo/ pdb-redo/ downloads the current entries.
• rsync -av rsync://rsync.pdb-redo.eu/pdb-redo/ pdb-redo/ downloads the entire archive.

License

Here you can find the data usage license.

PDB-REDO entry description

Each PDB-REDO entry consists of a set of files that describe the structure model in different states (original, re-refined, and re-refined & rebuilt). Some of the data is provided for easy data mining. The table below shows the typical URLs of the files for the fictitious entry 9xyz.