JMOL SIMULATION HOW TO

Because Jmol's interface is derived from Rasmol and Chime, the resources available for these two applications are useful for leaning how to use Jmol. To obtain more information on Jmol, view demos and obtain the tools needed for running Jmol as a standalone application or to develop websites with embedded Jmol images, visit the Jmol site at. To learn more about the development of Jmol please refer to an article by Angel Herraez that was published recently in Biochemistry and Molecular Biology Education (August, 2006).

JMOL SIMULATION MAC OS X

The standalone version can be obtained free of charge and runs under Windows, Mac OS X and Linux. Because it is Java based is essentially independent of the platform that it runs on, when used from a web page it requires only a Java enabled browser. It can be run as either a standalone application like Rasmol or embedded in webpages like Chime. It is an open-source, Java based application that has the same look and feel as Rasmol and Chime and can interpret all of the Rasmol and Chime commands. During this time a new application called Jmol has emerged as a viable replacement for both Rasmol and Chime. Rasmol and Chime complement each other nicely, with Rasmol being used by web developers to create and test the Rasmol scripts that they plan to use with Chime.Įven though both Rasmol and Chime have seen wide acceptance, further development of both these applications have languished since the turn of the millennium and are now longer compatible with many of the newer operating systems and browsers. Chime also has a pop-up menu that allows a visitor to a website to execute a subset of the Rasmol commands. These commands are either executed when a plug-in is loaded or can be activated by a visitor to the site using buttons and other control elements. For Chime the commands are coded into the web page by its author. For Rasmol the commands are entered from a command line with a subset of the commands available from the menu bar. Both Rasmol and Chime use the same command library for loading and manipulating molecular modes.

JMOL SIMULATION CODE

Chime was developed at Molecular Design Limited (MDL) and took the Rasmol code and modified it so that it could be used as a web browser plug-in to display three-dimensional, interactive molecular models from webpages. There are versions available for Windows, Unix and older versions of MacOS (prior to MacOS X). Rasmol was written in the early 1990's by Roger Sayle as a standalone application and was distributed free of charge. Over past couple of years Jmol has emerged as a viable replacement for two long-standing tools used for visualizing macromolecules on personal computers, Rasmol and Chime.

Jmol is a Java-based molecular modeling application that can be used either in a stand-alone mode, or as an embedded object in webpages.

These are show as spacefilling models and colored to atom type. Bound to the enzyme is fructose-1,6-bisphosphate, which is an allosteric effector for the enzyme, and phlosphoglycolic acid, which is a substrate analogue and inhibitor for the enzyme. The protein is modeled as a cartoon and colored to highlight the secondary structure of the protein. Figure: Shown above is a Jmol model for the enzyme pyruvate kinase, which catalyzes the last reaction in the glycolytic pathway.

Jmol simulation