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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 . 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. 29 Aug This is the primary home and download site for the Jmol Tutorial-Authoring Template (JTAT), which was released in , and updated in

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The console window is also available when Jmol is embedded into a web page. The latest version of Jmol can be obtained from the Jmol site. Both Rasmol and Chime use the same command library for loading and manipulating molecular modes.

In the standalone version of Jmol there are three ways enter commands.

Getting Started in Jmol

These are show as spacefilling models and colored to atom type. The tutorial must be uploaded to a server to provide online access, or the tutorial can be shown offline. If you are using a one-button mouse on a Mac, a ctrl-click can be used instead.

This tutorial was written for Jmol version Considerably more challenging to use than Proteopedia, but you have more control and the product tutorial is more user friendly.


Green Fluorescent Proteins create bioluminescence in animals like jellyfish. In this menu, click on the button ” Console ” which will open the Jmol Console.

Ligands are displayed in Ball and Stick Formatwhile ions or individual water molecules are displayed in Spacefill Format. The Jmol Display Window below, left is used to view your 3-dimensional protein or molecular structure.

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. The number of atoms selected is shown in parentheses, on the menu, after the word Select.

Despite name, pdb files can be used to represent almost any molecule. It may or may not agree with the numbering in a different model of the same molecule, or with other published reports.

You may also go directly to firstglance. To launch Jmol, open the folder containing the Jmol.

Jmol Tutorials

Introduction Before you get started Creating models Commands Rendering. Once launched, Jmol will display two windows. Page last modified on August 29,at JmolShell Download a tutorial-development environment to create tutorials that will display in a web browser. Open the tuutorial that contains your. Proteopedia’s Scene Authoring Tools make this by far the easiest place to create tutoiral, zoomable molecular scenes which are instantly viewable and searchable by anyone.

For these Jmol Training Guide tutorials, we will be using Jmol to primarily view the. After making a selection, use Color on the menu to apply a plain color, or a color scheme.


Jmol Training Guide – MSOE Center for BioMolecular Modeling

Jmol Application ‘s Export to Web Page: Unless otherwise indicated, comparisons are by Eric Martz. To measure the distance between two atoms, double click on the first atom. Most people prefer a larger Display Window.

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.

The command line provides access to all the commands that are available tot Jmol and, therefore, is the most powerful way to enter commands. Tutoorial most common source of free.

Editing wiki text is easier than HTML. There is another console window that may open when Jmol is launched that is titled ” Jmol console”. To obtain more information on Ttorialview 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: Your tutorials can be protected from editing by others if you wish.

Although it is interesting to explore models and visualizations created by others, it is much more engaging to create your own!