Part 1 - Getting Started

The CBM Jmol Training Guide

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Introduction

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.

This Jmol Training Guide will cover the commands, techniques and tools needed to create molecular renderings, physical models using 3-D printing technologies, as well as Jmol animations for online tutorials or electronic posters.

Click on the images below to display example renderings of three common proteins in the Jmol display to the right. Note that this display is fully interactive and can be rotated by clicking and dragging with your mouse!

Hemoglobin Proteins safely carry oxygen in the blood.

Insulin Proteins help regulate sugar in the bloodstream.

Green Fluorescent Proteins create bioluminescence in animals like jellyfish.

Accessing Jmol

Jmol originated as a Java-based program to be run locally on your computer. But Jmol can also be embedded into a webpage to be viewed with a browser such as Firefox, Internet Explorer, Safari and Chrome.

This Jmol Training Guide, along with all MSOE Center for BioMolecular Modeling programs, will use such a webpage. The Jmol Design Environment webpage, linked to below, will allow you to practice all of the commands, techniques and tools described throughout this Training Guide.

http://cbm.msoe.edu/markMyweb/jmolDesignEnvironment

Layout of the Jmol Design Environment Webpage

The Jmol Design Environment webpage is comprised of several main areas, described in more detail below.

  1. The Title Bar - This area contains the CBM logo, title of the Jmol Design Environment, and a few useful links to learn more about the CBM and this webpage.
  2. The Jmol Display Window - This is where the interactive display of your molecular structure will be displayed.
  3. The Jmol Console - This is where commands will be entered to manipulate how your molecular structure is being rendered.
  4. The Tool Column - This area contains a number of expandable menus that will be used for loading molecular structures, saving designs, and submitting designs to the CBM.


Contents of the Jmol Training Guide

The Jmol Training Guide is broken up into several sections.

If this is your first time exploring molecular structures with Jmol or participating in an MSOE Center for BioMolecular Modeling program, we encourage you to go through the Training Guide in order.

Skip Audio or Animation
Jmol Console