HSLS Update

FirstGlance in Jmol: A Free Web-based 3D Structure Visualization Tool

A picture is worth of thousand words — and when a picture provides a three-dimensional representation of an object, it becomes an invaluable tool for educators and researchers in the field of molecular sciences. Computer based molecule visualization software applications are increasingly important in areas ranging from general chemistry to computational chemistry, from inorganic chemistry to molecular biology, and from mineralogy to crystallography.

A key development in the history of molecular graphics programs was the release of RasMol. It was developed by Roger Sayle, who released the copyright to the public domain, and posted the source code on the Internet in 1993. Loaded with useful features such as ability to display important aspects of the molecular structure like alpha-helix, beta-pleated sheets, and hydrogen bonds, RasMol became one of the most popular and widely used molecular graphics programs in the world.

But RasMol, a stand alone software that requires downloading and installation on a user’s computer, was limited to use by only the computer savvy. By the mid-1990s, with the increasing popularity of Internet, there was a growing demand among educators and researchers for a Web-based method of displaying 3D structures of molecules. This unmet need was filled by the release of Jmol in December 2004. Jmol is a free open-source molecule viewer written in the Java programming language that works on multiple platforms, including Windows, Mac OSX, and Linux/Unix systems. When a user visits a Web page containing the Jmol applet, the program is automatically downloaded and executed on the client’s browser without requiring installation.

Following the precedent set by RasMol, Jmol has been used in biochemistry and molecular biology in various applications including FirstGlance in Jmol, a free Web-based tool for three-dimensional molecular visualization. It was developed by Eric Martz in the Department of Microbiology, University of Massachusetts at Amherst, and is available at <www.bioinformatics.org/firstglance>. It works in most popular browsers and platforms, including Internet Explorer or Firefox on Windows, and Safari and Firefox on Mac OSX.

In FirstGlance, the 3D structure of a molecule appears initially as a cartoon. By clicking on the links and buttons from the convenient control panel in the upper left corner, one can link to different renderings of the molecule. In addition to the cartoon format, molecules can be displayed in these formats, and several others:
·  Secondary Structures: shows alpha-helices and  beta-strands
·  N-C Rainbow: provides smoothed backbone traces, with nucleic acids thicker than proteins
·  Composition: provides space filling spheres of van der Waals radii
·  Vines: displays all amino acid side chains and nucleotide bases as sticks colored by atom types.

Settings can be turned on or off to show or hide ligands or water molecules. Users can also zoom in and out, or change the background color. Structures can be rotated or be made to spin by clicking the spin button. Help documents about each view or operation, including color keys, are always available in the lower left corner of the screen.

Online journal publishers have begun to employ Jmol technology. Nature Structural & Molecular Biology recently began including links from its table of contents to the FirstGlance 3D structures discussed in the articles.

The advantage of FirstGlance is that, unlike RasMol, you don’t need to be computer savvy to operate it. Consider using FirstGlance to help interpret experimental data and assist in the design of experiments based on your structure of interest.

--Ansuman Chattopadhyay