Chimera - Molecular Modeling software

PRETTY PICTURES PRETTY FAST. 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 “chimera_movie.mov” 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.

Reference : Education corner , spring 2008, RCSB Newsletter, Number 37.