News on 2010-05-06
As part of the structure annotation process, wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking. Beginning May 17, 2010 these documents will be available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors.
As these PDB validation reports provide an assessment of structure quality while keeping the coordinate file confidential, we encourage journal editors and referees to request them from depositors as part of the manuscript submission and review process. PDB validation reports are already required by the International Union of Crystallography (IUCr) journals as part of their submission process (see Baker et al. (2010) Acta Cryst. F66: 112 ). The reports are date-stamped, and display the wwPDB processing site logo. They contain essentially the same information, regardless of PDB annotation site. The validation reports will continue to be developed and improved as we receive recommendations from our Validation Task Forces for X-ray, NMR, EM, and small angle scattering methods, and as we further develop our data deposition and processing procedures.
Questions about these reports and the annotation process may be sent to us or info@wwpdb.org.
Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010
With the June 30, 2010 update, a new set of NMR restraint data files will be added to the wwPDB FTP archive ( ftp://ftp.wwpdb.org, ftp://ftp.ebi.ac.uk, and ftp://pdb.protein.osaka-u.ac.jp ). These restraint files, which will be identified as Version 2 files, are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom-level correspondences to the NMR model coordinate files in the current wwPDB archive. Restraint files containing restraint data as originally deposited (Version 1 files) will remain on the site and will continue to be updated regularly as new NMR entries are released.
About Version 2 Restraint Files
The Version 2 NMR restraint files were generated for the wwPDB by the BMRB in collaboration with PDBe and the Centre for Molecular and Biomolecular Informatics/Institute for Molecules and Materials at the Radboud University Nijmegen.
NMR restraints were parsed from their original format (Version 1), and harmonized with the coordinates using the software packages Wattos ( BMRB and CMBI / IMM ), FormatConverter and NMRStarExport ( PDBe ), and the CCPN framework.
The complexity of this process may have lead to minor modifications or loss of data in the Version 2 restraint files due to parsing or conversion errors. The PDB coordinate file and the Version 1 restraint files remain the primary reference for these data.
More information about the process used to generate these files is available (1-3).
Changes to wwPDB FTP Server
The initial release of the Version 2 NMR restraint files will add approximately 5625 new files (310 Mbytes) to the wwPDB FTP site. Version 2 restraint files for new PDB entries will be processed and made available after the PDB entry has been released. Version 1 restraint files for new PDB entries will continue to be released weekly.
NMR restraint files are named using extension .mr, as in "1abc.mr.gz" for PDB ID 1abc. Version 2 restraint files will be named "1abc_mr.str.gz", where "str" identifies the NMR-STAR (V3.1) data format. All restraint files are compressed (.gz) using the GNU gzip program.
Version 2 restraint files will be stored in a new directory path, grouped by the middle two
characters of the 4-character PDB ID:
ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/data/structures/divided/nmr_restraints_v2/
All of these data files will be symbolically linked to a single directory:
ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/data/structures/all/nmr_restraints_v2/
Version 1 restraint files will remain in their current directory structure.
For questions, please contact us or info@wwpdb.org.
References
- JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL Markley, and EL Ulrich (2005). BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12.
- WF Vranken, W Boucher, TJ Stevens, RH Fogh, A Pajon, M Llinas, EL Ulrich, JL Markley, J Ionides, and ED Laue (2005). The CCPN data model for NMR spectroscopy: development of a software pipeline . Proteins 59, 687-696.
- JF Doreleijers, WF Vranken, C Schulte, J Lin, JR Wedell, CJ Penkett, GW Vuister, G Vriend, JL Markley, and EL Ulrich (2009). The NMR Restraints Grid at BMRB for 5,266 Protein and Nucleic Acid PDB Entries. J Biomol. NMR 45, 389-396.
