Note: JSmol is a new version of Jmol that can run without Java. Jmol and JSmol are essentially the same program, and these names are sometimes used interchangeably. Drag the jmodel folder from the zip file into the folder you opened in the first step. Rename the folder immediately with your tutorial name, which should be as follows: the authors' first and last initials, all capital letters, in the same order you will use on your main page i. Then open the folder.
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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. 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 's by Roger Sayle as a standalone application and was distributed free of charge. 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. 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, 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 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. 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.
Menu Bar: The Jmol window has a menu bar with a very limited number of commands. The convention that will be used for entering a command from the menu bar will be, for example:. Click here to see how it looks. The popup menus are also available when Jmol is embedded into a web page. Command Line: One of the items in the popup menu is "Console 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 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. Forward to: Before you get started.
Getting Started in Jmol
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.
Click Here to download this tutorial as a PDF. Physical models of proteins are powerful tools that can be used synergistically with computer visualizations to explore protein structure and function. Although it is interesting to explore models and visualizations created by others, it is much more engaging to create your own! At the MSOE Center for BioMolecular Modeling we use the molecular visualization program Jmol to explore protein and molecular structures in fully interactive 3-dimensional displays. Jmol a free, open source molecular visualization program used by students, educators and researchers internationally.