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

Fall 2009
Number 43

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Data Deposition
SF-Tool: A Tool for Crystallographic Experimental Data Validation
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Deposition Statistics
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Outreach and Education
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Turn Your Computer into a PDB Structure Kiosk
Education Corner
Gary M. Battle, Ph.D.: Symposium on the Applications of Small-molecule Crystal Structure Information in Chemical Education
PDB Community Focus
Roland L. Dunbrack, Jr., Ph.D., Fox Chase Cancer Center


Gary M. Battle completed a Ph.D. in synthetic organic chemistry with Dr. Andrew Clark at the University of Warwick, UK in 2002, and subsequently joined the Cambridge Crystallographic Data Centre (CCDC; where he is now a Senior Applications and Research Scientist. In addition to providing user support and training on CCDC's full suite of software tools, Gary also leads the Centre's educational outreach activities. Gary’s work has been focused on the Teaching Database–a free 500-structure subset of the Cambridge Structural Database (CSD). This resource offers a 500-structure teaching database of a wide variety of molecules (from adrenaline to zirconium complexes) that can be used to enhance learning across the chemistry curriculum. To learn about this and other teaching tools offered by the CCDC, please visit

Symposium on the Applications of Small-molecule Crystal Structure Information in Chemical Education by Gary M. Battle, Ph.D.

As the use of crystal structure information continues to broaden, the Cambridge Structural Database (CSD) has become an indispensable resource for educators involved in both undergraduate teaching and research. This rapidly developing area was the focus of a symposium at the 238th national meeting of the American Chemical Society in Washington, D.C. on August 19, 2009. Featuring presentations from prominent educators, the symposium showcased ways in which the CSD is being used to enhance student learning across the entire span of the chemistry curriculum.

The value and availability of crystal structure information...

Frank Allen, who is now an emeritus research fellow at the CCDC, opened the symposium by highlighting the unique advantages that small molecule crystal structure information offers chemistry teachers. The benefits of visualizing and manipulating a diverse range of ‘real’ 3D structures onscreen and the pedagogical value of using experimentally measured data were explained. Guy Crundwell from Central Connecticut State University then discussed how using raw data mined from the CSD challenges his students to think more critically about the fundamental topics of bonding and molecular structure. In addition to this, Gary Battle from CCDC (your author) presented a number of free teaching resources, including a carefully compiled online interactive teaching subset of the CSD (
) and a number of associated tutorial exercises. John Woolcock of Indiana University of Pennsylvania also explained how WebCSD (the online search interface to the CSD) was used to great effect during the American Crystallographic Association (ACA) intensive ten-day summer course.

Exploring concepts of symmetry...

A highlight of the symposium was a presentation from Dean Johnston of Otterbein College. Dean introduced and demonstrated the online Symmetry Resources at Otterbein College ( The resources contained within this excellent website are designed to help students learn concepts of molecular symmetry and to help faculty teach these concepts. A point-group symmetry tutorial with interactive displays and animations guides students through a number of symmetry elements and operations. A gallery of 70 unique molecules with interactive display of symmetry elements and animation of operations is well worth a look. Finally, the ‘symmetry challenge’ includes an interactive flow chart that can be used to test and follow the process of determining the point group of a particular molecule–a great way to practice. Dean used CSDSymmetry (, a freely available database of symmetry-related information from CCDC, to identify interesting molecules with unique point groups for inclusion on his website.

Continuing this theme, St. Olaf College’s Bob Hanson demonstrated some brand-new crystallographic symmetry capabilities within Jmol (the widely used open-source Java viewer for 3D chemical structures) that were introduced specifically for this symposium. These features can be viewed in the Jmol Crystal Symmetry Explorer at

Display of symmetry elements in YbI2(THF)5 from Dean Johnston’s symmetry gallery

Broad appeal...

Speakers from a variety of disciplines contributed to the symposium, demonstrating the utility of crystallographic information across the whole of the chemistry curriculum.

Kraig Wheeler (Eastern Illinois University) spoke about conceptualizing reaction mechanisms using crystallographic data, and highlighted several examples of how crystallographic data can serve to support existing reaction theories and unravel mechanistic details in the organic classroom. Katherine Kantardjieff of California State University Fullerton presented a guide for users and consumers of crystallographic information from a biochemical perspective. Stephen Koch from State University of New York at Stony Brook gave an enthusiastic talk on how students in general chemistry through to advanced inorganic chemistry classes use the CSD to explore the diverse structural chemistry of molecular inorganic compounds. Also, Virginia Pett from the College of Wooster discussed how her physical chemistry students use the CSD in computer-based laboratory sessions.

Spreading the word...

The symposium concluded with examples of how CSD-based teaching resources and materials are being disseminated and shared within the educational community.

Illinois State University’s Gregory Ferrence summarized a two-year project supported by an NSF-funded Discovery Corps Fellowship. The grant has provided full Cambridge Structural Database System (CSDS) access to more than 30 Primarily Undergraduate Institutions (PUIs) in the USA and has enabled Greg to visit many of these universities and colleges to provide training and workshops, and to encourage others to develop their own CSDS-based educational materials.

Barbara Reisner from James Madison University provided an overview of IONiC (Intellectual Online Network of Inorganic Chemists), a vibrant virtual 'community of practice’ that facilitates collaborative development of learning materials and their dissemination to the wider inorganic community. Their website, VIPEr (Virtual Inorganic Pedagogical Electronic Resource,, serves both as a repository and as a user-friendly platform that facilitates virtual collaboration and community building. VIPEr already features a number of excellent CSD-based teaching exercises and activities.

Full symposium details including copies of the presentations are available from the CCDC website We would also be happy to learn of any other examples where the CSD is used in teaching at

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