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.
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.
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/zipped downloads all files of a PDB-REDO entry.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.
Here you can find the data usage license.
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.
| 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) |