Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Fall 2011
Number 51
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Message from the RCSB PDB
Data Deposition
Deposition Statistics
Validate Structure Factor Diffraction Data with SF-Tool
New pdb_extract Release
wwPDB News
Data Query, Reporting and Access
Website Statistics
New Website Release
Different Ways To Explore New Entries
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Christopher M. Smith, Ph.D., The Anatomy of Vision: Insights into Molecular Modeling for the Middle Schooler


Deposition Statistics

From July 1 - September 30, 2011, 2393 experimentally-determined structures were deposited to the PDB archive. The entries were processed and annotated by wwPDB teams at the RCSB PDB, PDBe, and PDBj. 6939 have been deposited overall in 2011.

During the same time quarter, 2025 structures were released in the PDB.

Of the structures deposited in 2011 so far, 79.9% were deposited with a release status of "hold until publication"; 17.9% were released as soon as annotation of the entry was complete; and 2.2% were held until a particular date. 92.8% of these entries were determined by X-ray crystallographic methods; 6.3% were determined by NMR methods.

Validate Structure Factor Diffraction Data with SF-Tool

SF-Tool is a streamlined, web-based tool for validating structure factor diffraction data files. The latest release includes support for neutron and hybrid experiments; incorporates checks from REFMAC1, PHENIX2, and SFCHECK3; and converts multiple data sets into a single mmCIF file.

Visit to:

  • Validate model coordinates against structure factor data for X-ray and neutron data
  • Easily convert structure factor files between different formats (mmCIF, MTZ, CNS/CNX, XPLOR, SHELX, TNT, HKL2000, SCALEPACK, D*Trek, SAINT, and more)
  • Check for and validate twinned or detwinned data

Documentation for this program is available. Questions, comments, and suggestions should be sent to

New pdb_extract Release

Version 3.11 of pdb_extract has been released as an online web tool and a downloadable workstation program.

pdb_extract minimizes errors and saves time during the deposition process by extracting key details from the output files produced by many X-ray crystallographic and NMR applications. The program merges these data into macromolecular Crystallographic Information File (mmCIF) data files that can be used with ADIT for validation and deposition.

New features include:

  • Supports data from hybrid method experiments
  • Parses NCS and TLS ranges in BUSTER and REFMAC
  • Improved mtz to mmCIF conversion
  • Assesses quality of X-ray data

Complete details are available in the release notes and manual. Tutorials are available.
Depositors can upload files into the pdb_extract webserver or download the latest workstation version at

wwPDB News

Archive Version 4.0 Released

PDB Archive Version 4.0 was released in July. These files follow the PDB Exchange Dictionary v.4.0 and contain the results of remediating complex problems, including the representation of biological assemblies, residual B factors, peptide inhibitors and antibiotics, and entries in nonstandard crystal frames.

For PDB format files, only the entries changed during this remediation have been updated (<17000). These changes are identified as version 3.3 of the PDB file format. All files in PDBx/mmCIF and PDBML/XML formats reflect the new schema updates. Any changes made to the data are recorded in the PDBX_VERSION data category.

From July 13, 2011 onward, all new releases and modified entries will follow the updated formats. Revisions to released entries will be tracked and numbered in the PDBx/mmCIF formatted files.

A description of the review and resulting changes and corrections is available from the wwPDB website ( These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.
















1. Refinement of Macromolecular Structures by the Maximum-Likelihood Method. G.N. Murshudov, A.A. Vaguine, E.J. Dodson (1997) Acta Cryst. D53: 240-255.

2. PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger, P. H. Zwart (2010) Acta Cryst. D66: 213-221

3. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. A.A. Vaguine, J. Richelle, S.J. Wodak (1999) Acta Cryst. D55: 191-205.


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