This is the primary home and download site for the Jmol Tutorial-Authoring Template (JTAT), which was released in , and updated in Jmol Tutorial. Jmol is a free open source applet developed by the people at www. for the interactive display of molecules in web browsers. No plugins. Tutorial for using Jmol with course pages in Biochemistry I ( & ) at Carnegie Mellon University.

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Shown above is a Jmol model for the enzyme pyruvate kinase, which catalyzes the last reaction in the glycolytic pathway. There is another console window that may open when Jmol is launched that is titled ” Jmol console”. This page provides instructions for installing and running Jmol.

Chime also has a pop-up menu that allows a visitor to a website to execute a subset of the Rasmol commands. The Jmol download page is located at http: Despite name, pdb files can be used to represent jmool any molecule. Your tutorial will include a slider for zooming or slabbingspin toggle and centering buttons, details that display only when requested, and “How To” put views in Powerpoint slides, etc.

Your tutorials can be protected from editing by others if you wish. Jmol is capable of using many different sources files for creating molecular tuotrial. In the standalone version of Jmol there are three ways enter commands.


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 tutoriao to display three-dimensional, interactive molecular models from webpages. These are show as spacefilling models and colored to atom type. The latest version of Jmol can be obtained from the Jmol site.

MSOE Center for BioMolecular Modeling – Jmol Tutorial Creator

The console window is also available when Tktorial is embedded into a web page. Please send suggestions for improvement to the email above. It can be run as either a standalone application like Rasmol or embedded in webpages like Chime. To obtain more information on Jmolview 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: Recent Changes All Admin.

Those known to me are listed below. Here you can create customized molecular scenes, which will be online immediately.

Both Tutorisl and Chime use the same command library for loading and manipulating molecular modes. Before you get started.

The Rasmol Homepage is a good location to find these resources. Introduction Before you get started Creating models Commands Rendering.

Unless otherwise indicated, comparisons are by Eric Martz. The development of Jmol is currently proceeding at a heady pace, so we can expect this version to tuutorial be supplanted by newer version with expanded capabilities. The popup menus are also available when Jmol is embedded into a web page.


Obtaining, Installing and Using Jmol Two things are required to view the molecules in this tutorial; java must be installed on the computer, and javascript must be enabled in the browser used to view the tutorials. The protein is modeled as a cartoon and colored to highlight the secondary structure of the protein. 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.

Some tutorials require that the individual download and view pdb files of the molecules described in the tutorial.

Jmol Tutorials

If you are using a one-button mouse nmol a Mac, a ctrl-click can be used instead. Editing wiki text is easier than HTML. Jmol What is Jmol? Proteopedia’s Scene Authoring Tools make this by far the easiest place to create rotatable, zoomable molecular scenes which are instantly viewable and searchable by anyone.

This tutorial was written for Jmol version