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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:

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

  • wget https://pdb-redo.eu/db/9xyz/9xyz_final.pdb downloads the fully optimised (re-refined and rebuilt) PDB 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.zip downloads all files of a PDB-REDO entry.

Download entire PDB-REDO databank using rsync:

  • 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.


PDB_REDO data files
Description Typical URL (for fictitious entry 9xyz)
Atomic coordinates
Initial model https://pdb-redo.eu/db/9xyz/9xyz_0cyc.pdb.gz
Re-refined (only) model https://pdb-redo.eu/db/9xyz/9xyz_besttls.pdb.gz
Re-refined & rebuilt structure model https://pdb-redo.eu/db/9xyz/9xyz_final.pdb
Re-refined & rebuilt structure model with total B-factors (PDB) https://pdb-redo.eu/db/9xyz/9xyz_final_tot.pdb
Re-refined & rebuilt structure model with total B-factors (mmCIF) https://pdb-redo.eu/db/9xyz/9xyz_final.cif
Electron density
Map coefficients for the original model https://pdb-redo.eu/db/9xyz/9xyz_0cyc.mtz.gz
Map coefficients for re-refined (only) model https://pdb-redo.eu/db/9xyz/9xyz_besttls.mtz.gz
Map coefficients for re-refined & rebuilt structure model https://pdb-redo.eu/db/9xyz/9xyz_final.mtz
Validation data
WHAT_CHECK report for initial model https://pdb-redo.eu/db/9xyz/wo/pdbout.txt
WHAT_CHECK report for re-refined (only) model https://pdb-redo.eu/db/9xyz/wc/pdbout.txt
WHAT_CHECK report for re-refined & rebuilt model https://pdb-redo.eu/db/9xyz/wf/pdbout.txt
Ligand and ligand interaction data for the initial and re-refined & rebuilt structure model https://pdb-redo.eu/db/9xyz/9xyz_ligval.json (only for entries with ligands; JSON Schema)
Map fitting scores for the initial model
(RSCC, RSR, EDIAm, OPIA)		 https://pdb-redo.eu/db/9xyz/9xyz_0cyc.json.gz (JSON Schema)
Map fitting scores for the re-refined & rebuilt model https://pdb-redo.eu/db/9xyz/9xyz_final.json (JSON Schema)
Data for model improvement sliders https://pdb-redo.eu/db/9xyz/pdbe.json (JSON Schema)
Visual tools
COOT script to show model changes https://pdb-redo.eu/db/9xyz/9xyz_final.py (Python) or https://pdb-redo.eu/db/9xyz/9xyz_final.scm (Scheme)
Descriptive data
PDB-REDO statistics for data mining (crystal parameters, R-factors, validation scores, etc.) https://pdb-redo.eu/db/9xyz/data.json (JSON Schema)
List of homologous entries in PDB-REDO databank https://pdb-redo.eu/db/9xyz/9xyz_available_homologs.json (JSON Schema)
DSSP analysis of the re-refined & rebuilt model https://pdb-redo.eu/db/9xyz/9xyz_final.dssp
Software versions of all programs used https://pdb-redo.eu/db/9xyz/versions.json (JSON Schema)