Downloads

PDB_REDO software

PDB_REDO consists of a (tc)shell script that calls many programs. Some of these programs are PDB_REDO-specific and can be downloaded directly. Others are licensed and need to be downloaded elsewhere. All software used is free for academic usage.

• PDB_REDO script and programs, see the header for configuration and usage.
• CCP4.
• WHAT_CHECK.
• Refmac, comes with the CCP4 package but we use the latest version.
• ARP/wARP.
• PDB-care.

If you have questions about running PDB_REDO, feel free to e-mail.

PDB_REDO entries

You can load the optimised structures and electron density maps straight into (Win)Coot.

• How to install:
  • Coot (for Linux and OSX):
    1. Download the PDB_REDO plugin for Coot (courtesy of Paul Emsley) into the "scheme" directory in your Coot installation, located at $COOT/share/coot/scheme/.
    2. Open the file coot.scm in that same directory with a text editor.
    3. Change "ncs.scm"
"parse-pisa-xml.scm" to "ncs.scm"
"pdb_redo.scm"
"parse-pisa-xml.scm" and save the file.
  • WinCoot (and Coot without scheme)
    1. Download the PDB_REDO plugin for WinCoot into the "python" directory in your Coot installation, typically located at C:\WinCoot\share\coot\python\.
    2. Open the file coot_load_modules.py in that same directory with WordPad.
    3. Change "extensions.py",
"shelx_extensions.py", to "extensions.py",
"pdb_redo.py",
"shelx_extensions.py", and save the file.
• How to use:
  1. When you start Coot there should be a button "PDB_REDO" on the menu bar. Click it, then click "Fetch fully optimised PDB from PDB_REDO..." and type the PDB id (in small letters) in the box. Click 'Fetch!"
  2. You can also try using the "Fetch conservatively optimised PDB from PDB_REDO..." option if a fully optimised structure model is not yet available.
  3. You may need to center on an atom to get a good view of the structure model. Enjoy.

You can download single PDB_REDO entries via the website or using wget. Examples:

• wget www.cmbi.ru.nl/pdb_redo/xy/9xyz/9xyz_final.pdb downloads the fully optimised PDB file.
• wget www.cmbi.ru.nl/pdb_redo/xy/9xyz/9xyz_besttls.pdb downloads the conservatively optimised PDB file.
• wget www.cmbi.ru.nl/pdb_redo/xy/9xyz/9xyz_reref.tar.bz2 downloads the PDB files, MTZ files, TLS files, and more in a single compressed file.

You can download all PDB_REDO entries using rsync. Example:

• rsync -avz --delete rsync://rsync.cmbi.ru.nl/pdb_redo/ my-pdb_redo/ downloads the entire archive.
• rsync -avW --delete --filter '+ **/' --filter '+ *.pdb' --filter '- *' --prune-empty-dirs rsync://rsync.cmbi.ru.nl/pdb_redo/ my-pdb_redo downloads only the optimised PDB files.