Dear CCP4BB subscribers, We are happy to announce the release of PDB_REDO version 6.
PDB_REDO is a pipeline for crystallographic structure model optimisation, and you can use it through: 1. The PDB_REDO webserver at http://xtal.nki.nl/PDB_REDO 2. Local installations available for Linux (www.cmbi.ru.nl/pdb_redo/pdb_redo.tar.bz2) and now also for OSX (www.cmbi.ru.nl/pdb_redo/pdb_redo_osx.tar.bz2). PDB_REDO refines any structure model you are working on by optimising REFMAC refinement and by partial model rebuilding. The process is fully automated so you only need to provide an initial structure model and your reflection data. PDB_REDO will give you a new structure model, MTZ files for new maps, a validation report, optimised parameters for running REFMAC in the future, and COOT scripts to walk you through the structural changes. New features include: - All major refinement parameterisation steps (for geometric and B-factor restraint weights, B-factor model selection, TLS model selection) are now parallelised. This option can give a 4-fold speed-up for a typical PDB_REDO run. - External REFMAC restraints (e.g. from proSMART) can be added to PDB_REDO jobs. - Base pair and planarity restraints from LibG can be generated on-the-fly for structures with nucleic acids. - Detection of changes in the cis/trans state of peptides, and visualisation in COOT. - Improved handling of carbohydrates by automatic nomenclature and LINK record fixing. - Improved handling of LINK records. - More options to customise your job, e.g. to use tighter-than-default restraints. - Improved cross validation now also reports R-complete (courtesy of Tim Gruene) - Scalable plots for validation report for 1. per-residue change of RSCC 2. model quality with respect to the PDB and PDB_REDO databanks Licensing: PDB_REDO is free to all academic and commercial users, but licences for other programs in the pipeline (e.g. for CCP4) may be required. Users of the server only need a valid CCP4 license. The developers of YASARA and FoldX have waved any licence requirements for their software on the server. Developers in the PDB_REDO project: Amsterdam: Robbie Joosten, Bart van Beusekom, Krista Joosten, Anastassis Perrakis Nijmegen: Wouter Touw, Gert Vriend Cambridge: Fei Long and Garib Murshudov Special thanks to: Doug Kuntz, Luca Jovine, and Richard Bunker for requesting and testing some of the new features Netherlands Organisation for Scientific Research for funding the project For more information see: http://www.cmbi.ru.nl/pdb_redo or http://xtal.nki.nl/PDB_REDO Best wishes, Robbie and Tassos
