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

Winter 2009
Number 40

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Message from the RCSB PDB
Data Deposition
PDB Archive Version 3.15 to be Released
Tips for Depositing Multiple Related Structures using ADIT/ADIT-NMR
2008 Deposition Statistics
Data Query, Reporting and Access
2008 Website Statistics
View Domain Annotations in 3D
Getting Started with the RCSB PDB Website
Browser Check for Compatibility with Website Features
Outreach and Education
Meetings and Presentations
Looking at Structures: A Resource for Learning About PDB Data
Publications: 2008 Annual Report and more
Education Corner
Bernadette Uzzi, Coordinator, The Science Learning Center at Brookhaven National Laboratory
PDB Community Focus
Johannes Kirchmair, Ph.D., and Gerhard Wolber, Ph.D., University of Innsbruck

Outreach and Education

RCSB PDB Meetings and Presentations

The RCSB PDB has been participating in a wide variety of meetings:

  • At the New Jersey Science Convention (NJSC; October 14-15; Somerset, NJ), science teachers visiting the RCSB PDB booth learned about the structures in the PDB archive and the RCSB PDB materials available for use in their classrooms. Many teachers also created virus structures during a presentation by Shuchismita Dutta.

Many teachers created virus structures with the RCSB PDB at the New Jersey Science Convention.

  • John Westbrook described the Chemical Component Dictionary and Ligand Expo at the eCheminfo Community of Practice Meeting on Advances in Drug Discovery and Development (October 13-17; Philadelphia, PA).

  • During the meeting of the Association of Science and Technology Centers (ASTC; October 18-21; Philadelphia, PA), science museums representatives and content developers met David Goodsell and Christine Zardecki at the exhibit booth to learn about the resources available for visualizing structures available from the RCSB PDB.

At the Association of Science and Technology Centers meeting, science museum content developers picked up resources and materials at the RCSB PDB exhibit booth.

  • Huanwang Yang presented a poster about online tools such as pdb_extract and SF-Tools at the Pittsburgh Diffraction Conference (October 30-November 1; Pittsburgh, PA).

  • At the Cold Spring Harbor Course X-Ray Methods In Structural Biology (October 13-28), John Westbrook presented “PDB Tools in Deposition”.

  • Shuchismita Dutta described the evolving PDB resource and the wwPDB in a poster at the EMBO World Lecture Course Recent Developments in Macromolecular Crystallography (November 9-14, 2008; Pune, India).

Future meetings include the Keystone Symposia Frontiers of NMR in Biology (February 15 - 20, 2009; Santa Fe, NM) and the Biophysical Society Annual Meeting (February 28 - March 4, 2009; Boston, MA). The RCSB PDB will also be participating in the San Diego Science Festival and Rutgers Day this spring. Details will be announced at

Looking at Structures: A Resource for Learning About PDB Data

Where are all the hydrogen atoms in this file? Should I care about the R-factor? Why are there 20 overlapped structures in my file? These questions and many others are explored in the RCSB PDB's new Looking at Structures online resource.

Using text, images, and interactive Jmols, Looking at Structures intends to help researchers and educators get the most out of the PDB archive. Broad topics include how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges in exploring the archive. A Table of Contents appears on the right side of every page so at any time, users can access the individual pages: Biological Units, Dealing with Coordinates, Methods for Determining Structure, Missing Coordinates and Biological Units, Molecular Graphics Programs, Resolution, and R-value and R-free.

Looking at Structures is available from the General Education section of the left-hand menu at

From the Looking at Structures chapter on Dealing with Coordinates. The left image shows myoglobin (PDB entry 1mbo) using the default representation in MBT Protein Workshop. It shows a ribbon diagram for the protein, and ball-and-stick for the small molecules. In the right image, we have changed the representation to show all atoms, using the information in each atom record to color the molecules differently. This clearly shows the heme group in bright red, and a bound oxygen molecule in turquoise. (1mbo: S.E. Phillips (1980) Structure and refinement of oxymyoglobin at 1.6 Å resolution. J.Mol.Biol. 142: 531-554

Publications: 2008 Annual Report and more

This report cover highlights structures published in the Molecule of the Month series since January 2000.
The 2008 Annual Report features current progress and accomplishments, and explores the RCSB PDB's different activities in data deposition, query, and education.

The 2008 report highlights milestones, such as the publication of the 100th installment of the Molecule of the Month, and online resources such as Advanced Search. This publication is currently being distributed to the diverse community of PDB users in academia, industry, and education. If you would also like a printed copy, please send your postal address to

Interested in an Education Corner from an older newsletter? Want to know what papers have been published that discuss the RCSB PDB project? Looking for a flyer to guide you through the deposition process? The News and Publications page offers access to all RCSB PDB publications. Located in the General Information section of the left-hand menu, this page archives our Annual Reports on the history, mission, and yearly accomplishments of the project; publications in peer-reviewed journals; weekly news items about recent features and upcoming events; the quarterly newsletter; and more. Requests for printed copies may also be sent to

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