Introduction
Figure: Shown above is a Jmol model for the enzyme pyruvate kinase, which catalyzes the last reaction in the glycolytic pathway. The protein is modeled as a cartoon and colored to highlight the secondary structure of the protein. Bound to the enzyme is fructose-1,6-bisphosphate [FBP], which is an allosteric effector for the enzyme, and phlosphoglycolic acid [PGA], which is a substrate analogue and inhibitor for the enzyme. These are show as spacefilling models and colored to atom type.
Overview
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. 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. Rasmol was written in the early 1990's by Roger Sayle as a standalone application and was distributed free of charge. There are versions available for Windows, Unix and older versions of MacOS (prior to MacOS X). 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. Both Rasmol and Chime use the same command library for loading and manipulating molecular modes. For Rasmol the commands are entered from a command line with a subset of the commands available from the menu bar. For Chime the commands are coded into the web page by its author. 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. Chime also has a pop-up menu that allows a visitor to a website to execute a subset of the Rasmol commands. 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.
Even 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. During this time a new application called Jmol has emerged as a viable replacement for both Rasmol and 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. It can be run as either a standalone application like Rasmol or embedded in webpages like Chime. 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. The standalone version can be obtained free of charge and runs under Windows, Mac OS X and Linux. 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). 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 http://jmol.sourceforge.net/. 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. The Rasmol Homepage is a good location to find these resources.
This tutorial will focus on using Jmol as a standalone application for viewing and manipulating molecular structures. Jmol is capable of using many different sources files for creating molecular models. All these different source files are plain text files and contain the three-dimensional coordinates for the atoms in a structure along with other information for viewing these structures. In this tutorial we will use pdb files, which is the format that is used by the Protein Data Bank. Despite name, pdb files can be used to represent almost any molecule.
This tutorial was written for Jmol version 10.3.1. The development of Jmol is currently proceeding at a heady pace, so we can expect this version to soon be supplanted by newer version with expanded capabilities. The latest version of Jmol can be obtained from the Jmol site.
Conventions
<return> will be used to indicate pressing the Return key on a Mac keyboard or the Enter key on the QWERTY area (not the numeric keypad) of a PC keyboard
<right-click> will be used to indicate pressing right button on a two-button mouse on both Macs and PCs. If you are using a one-button mouse on a Mac, a ctrl-click can be used instead.
In this tutorial, the following conventions will be used for entering commands and using menus. In the standalone version of Jmol there are three ways enter commands.
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Menu Bar:File:Open (Instructs you to select "Open" from the "File" menu in the menu bar.) Click here to see how it looks.
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Popup Menus:Select>Protein>Backbone (Instructs you to select "Backbone" from the "Protein" popup menu, which is found by selecting "Select" from the popup menu that appears when you right-click on the Jmol window.) Click here to see how it looks.
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Command Line: One of the items in the popup menu is "Console...". Selecting this item will open a new window that is titled "Rasmol Scripts" that displays a "$" prompt. Commands are typed at the prompt and entered by pressing the <return> (Mac) or <enter> (PC) key on the computer keyboard. The console window is also available when Jmol is embedded into a web page. (Note: There is another console window that may open when Jmol is launched that is titled "Jmol console". The Rasmol Script console window can also be opened by selecting "Scripts..." from the "File" menu in the window bar. This window is not used for entering Jmol commands and can be closed.) The command line provides access to all the commands that are available tot Jmol and, therefore, is the most powerful way to enter commands.
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Command Line: $ color green <return> (Instructs you to type the command "color green" at the $ prompt and press the return key to enter the command.) Click here to see how it looks.
Filenames will be written in boldface -- for example, 1lui.pdb.
Forward to: Before you get started