Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank

Summer 2008
Number 38

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Data Deposition
SF-Tool: A Tool for Crystallographic Experimental Data Validation
Ligand Expo: A Small Molecule Resource
Workshop on Next Generation Validation Tools for the wwPDB
Deposition Statistics
Data Query, Reporting and Access
Website Statistics
Secondary Structure Information
RCSB PDB Usage Statistics
Outreach and Education
RCSB PDB Meetings and Presentations
RCSB PDB Poster Prize Awarded at ACA Meeting
Princeton High School Students Win New Jersey Science Olympiad Protein Modeling State Finals
Congratulations to National Tournament Champions
Papers Published
Structural Displays
Education Corner
Biochemistry and Molecular Biology Education, a Journal for University, College, and High School Educators by Judith G. Voet and Donald H. Voet
PDB Community Focus
John Norvell, Ph.D., National Institute of General Medical Sciences


SF-Tool: A Tool for Crystallographic Experimental Data Validation

A streamlined, web-based tool is available for validating crystallographic experimental data. SF-Tool ( can be used to:

  • Validate your model coordinates against structure factor data
  • Easily translate your structure factor file between different formats (mmCIF, MTZ, CNS/CNX, XPLOR, SHELX, TNT, HKL2000, SCALEPACK, D*Trek, SAINT, or OTHER format)
  • Check for twinned or detwinned data
Documentation for this program is available. Questions, comments, and suggestions should be sent to:

Ligand Expo: A Small Molecule Resource

The Chemical Component Dictionary archives chemical and structural information about all of the small molecules found within PDB structure entries. Ligand Expo is a new tool that can access, visualize, and build reports about these data.

With Ligand Expo, users can also

  • Search for a chemical component
  • Browse tables of components that contain
    • modified amino acids and nucleotides
    • popular drugs (trade and generic names)
    • common ring systems
  • Review related information in chemical dictionaries and resource files (chemistry, geometry, atom nomenclature, and more)
  • Download model and ideal chemical component coordinates
  • View all instances of a component in released PDB entries

A flyer describing Ligand Expo is available for download from the RCSB PDB website.

Ligand Expo ( is an update of the Ligand Depot resource.

Workshop on Next Generation Validation Tools for the wwPDB

A meeting of the wwPDB X-ray Validation Task Force was held to collect recommendations and develop consensus on additional validation that should be performed on PDB entries, and to identify software applications to perform validation tasks.

The workshop was organized by Randy Read (Cambridge University), and sponsored by the RCSB PDB & PDBe. Detailed information about the workshop is available at

Deposition Statistics

In the second quarter of 2008, 1689 experimentally-determined structures were deposited to the PDB archive. The entries were processed by wwPDB teams at the RCSB PDB, PDBe, and PDBj.

Of the structures deposited, 76.8% were deposited with a release status of "hold until publication"; 14.3% were released as soon as annotation of the entry was complete; and 8.9% were held until a particular date.

89.5% of these entries were determined by X-ray crystallographic methods; 9.5% were determined by NMR methods.

During the same time period, 2534 structures were released into the archive.

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