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

Spring 2008
Number 37

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Data Deposition
• sf-convert: A Format Conversion Tool for Structure Factor Files
• EmDep2: Deposit EM Maps at the MSD-EBI or RCSB PDB
• 2008 Deposition Statistics
• Data Processing Versioning Procedures

Data Query, Reporting and Access
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Outreach and Education
• RCSB PDB Celebrates Teaching, Learning, and More
• Protein Sculptures on Display at Rutgers
• Papers Published

Education Corner
Moving Pictures: Using Chimera to Make Molecular Multimedia for the Classroom by Dr. Jeramia Ory, Kings College

PDB Community Focus

Dr. Christine Orengo, University College London



Moving Pictures: Using Chimera to make molecular multimedia for the classroom by Dr. Jeramia Ory, Kings College

Jeramia Ory is an Assistant Professor in the Department of Biology at King’s College in Wilkes-Barre, Pennsylvania where he teaches Genetics, Biochemistry, and Systems Biology. His training is in X-ray crystallography and NMR spectroscopy, and he was previously a Biochemical Information Specialist at the RCSB PDB. While at the RCSB PDB, he produced numerous images for this newsletter, annual report and official documentation. The movies and figures he uses for class can be viewed on his homepage ( jeramiaory) in the “Multimedia” section, and are free for educational use.

Getting students to grasp the link between 3D structure and biological function is a necessary and challenging part of many undergraduate courses. Structural information can help students “get it” in a way that cannot be underestimated. As an example, numerous students have told me how much easier it is to understand stereochemistry when they can manipulate chemicals on a computer screen in 3D rather than trying to work out wedge/hash 2D conventions. As the number of structures in the PDB archive continues to grow, the challenge lies not in finding structural information related to the topic at hand (the Advanced Search on the RCSB PDB website is a great resource), but in incorporating the information into lecture materials and presentations without draining an instructor’s time or resources. Fortunately for instructors, a number of free programs that excel in molecular visualization and analysis are now available. Instead of reviewing the myriad of programs out there, I will focus the one I use to create multimedia presentations for my students–Chimera1.

CHIMERA is written and maintained by the Computer Graphics Lab at the University of California, San Francisco. It has a long history in molecular visualization, having started as a program designed in 1980 for high-end graphics workstations. What this means practically is that this research group has been thinking about the needs of the molecular visualization community for a long time. As modern desktop computing power has grown, the visualization community has expanded from its original base of X-ray crystallographers to educators and students as young as high school. While no program can be all things to all people, Chimera comes close. I have personally used it for hands on molecular visualization workshops with groups ranging from high school students to undergraduates with good results. Chimera has a few advantages when compared to other packages out there.

COST. Chimera is free for academic use. This is becoming less of a unique feature with the rise of open source and free software, but it is still an important consideration. After using Chimera for an exercise, I direct students to the download page so they can use it on their home computers if they wish to continue exploring. Just as important, Chimera is available for every major operating system: Windows, Macintosh and Linux (and more). Of course, as critics of free software are fond of saying, “free software is only free if your time has no value.” Luckily, the program is forgiving to new users, and rewards time spent with it.

The last thing educators have is time to waste. Chimera is a powerful analysis and visualization tool and is written with scientists in mind, however, it is quite easy to learn and new users can generally find their way around the program in about an hour. I run a protein visualization exercise in my undergraduate Biochemistry class that walks the students through the basics of Chimera; they align myoglobin and hemoglobin and then color the aligned residues by conservation (an example is shown below).

Myoglobin (2MM1) and hemoglobin (4HHB) aligned; residues are colored by conservation

Most students complete the exercise in 50 minutes and find it useful to be able to explore protein structure on their own. Should they not finish, the fact that it is free means they can finish up at the campus computer lab or at home. The program is well-documented online ( and comes with tutorials for new users.

SUPPORT. The Chimera community continues to grow as the program reaches different user groups. There is an active mailing list of Chimera users that shares ideas and problems, and is an excellent resource. Furthermore, the developers of the program monitor the list, and have been known to write modules for the program to deal with special users requests. These requests have even been known to make it into future releases as new features. One way or another, you can usually find someone willing to help you make the figures or movies you want.

Let’s face it, you can stand in front of a lecture hall for an hour, waving your arms, talking about the symmetrical relationships of hemoglobin’s four subunits, or you can display some nicely rendered images and a movie or two and get the same point across in five minutes. Say what you will about today’s students, they respond to multimedia and in some cases have grown to expect it. This is where Chimera shines. Once learned, gorgeous images take just a few minutes to set up and render. In my biochemistry class, I often make structural figures rather than using the textbooks illustrations, or load Chimera in class and walk students through the structure in 3D. This accomplishes two things: 1) I get to highlight what it is I find important in an RNA double helix, an enzyme active site, etc., and 2) it forces me to learn the structural landscape of the molecules rather than relying on the textbook. The rendering styles of Chimera are of course a matter of taste, but frequent readers of the RCSB PDB’s newsletter have already seen what Chimera can do; it is the “go to” program among the staff and is used on many official publications.

So, now that you are convinced to give Chimera a try, how do we make some movies? There are tutorials on the web site, but to start with, you can try this simple set of commands. In your favorite text editor (Notepad in Windows or TextEdit in Mac OS X), create a file called “movie.cmd” and enter the following text:

movie record
roll y 1 360
wait 360
movie stop
movie encode

Save the file, start Chimera and load your molecule of interest. Get it looking how you like, then open the file “movie.cmd” (File… Open…) and watch it go. This script will rotate the molecule about the y axis in 360 steps of 1 degree, then save the movie. When it’s done you should have a file named “” that you can show to your students. If you would like to see some of the movies I use in my Genetics and Biochemistry lectures, or if you would like to use them in your own classes, please visit my website.


  1. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin (2004) UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem. 25(13): 1605-12.


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