A Tutorial for
Using Jmol to Do Molecular Modeling

Creating Models

Getting Started

One of the huge advantages of using computers to create molecular models is the speed at which they can convert a list of atomic coordinates into a three-dimensional model. While looking at some of the models that we will be creating with Jmol, imagine building these with the ball and stick model kits that you have used to build models of small molecules. Building models with Jmol works a little differently than snapping balls and sticks together. With Jmol model building is a two step process: you first select the that atoms you wish to work with and then tell Jmol what you want to do with the atoms you have selected. This is done using commands.

In the Introduction we discussed that there are three ways to enter commands with the standalone version of Jmol:

There is a downside to this approach, however; you need to know what commands to type before you can type them. Those of you who have used computer operating systems for longer than a decade (two decades in the case of Macs), such as Unix or MS-DOS, know what this is like. Regardless, the upside of this method for interacting with Jmol far outweigh the downsides.


Launch Jmol by double-clicking on the icon for the Jmol.jar application file. After the application window opens, select Menu bar:File:Open. An open dialogue window should appear showing you the files that are located in the same folder as the Jmol.jar file. If you have placed the 1liu.pdb in this folder, you should see it, if not, you will need to navigate to its location. Select the 1liu.pdb structure file and click on the "Open" button. Voila!, a model for pyruvate kinase should appear on your screen. There is often another window that opens when you launch Jmol called the Jmole Console. This is used by Jmol to send messages back to the user. We will not be using this window so you can close it if you want. The Jmol Console window is different than the Rasmol Scripts console window, which is the window that contains the command line for entering commands.

By default, when Jmol opens a structure file, it creates a ball and stick model, with the atoms represented as spheres (balls) with a radius that is 20% of the vander Waals radius and the bonds as sticks with a radius of 0.15 Angstroms. Click here to see what this should look like.

Moving around

To move the model around and zoom in on it use the following combinations of keys, clicks and drags. The coordinate system for the Jmol window have the x and y axes in the plane of the screen with the y-axis being vertical and the x-axis being horizontal. The z-axis comes out the page directly at the viewer.

Mousing Around

Rotation about the x and y axes Click and drag the mouse.
Left-right causes rotation about the y-axis
Up-down cause rotation about the x-axis
Rotation about the x-axis Shift-key, click and drag left-right
Zooming in and out Shift-key, click and drag up-down
Moving the model in the x-y plane Shift-key, double-click & hold and drag
Clip the model from the front (slab) Ctrl & Shift keys, click and drag up-down
Clip the model from behind (depth) Ctrl & Shift keys, double-click & hold, drag up-down
Center model and expand to fill screen Shift-key and double-click on background

Forward to: Commands

Back to: Before you get started

Go to:


Before you get started

Creating models