Introduction to Jmol

Welcome! This tutorial is designed to teach you how to explore a 3D molecular structure using Jmol, which is the program that displays the structure in each of the Structure Tutorials. We will focus on how to manipulate the 3D molecule in space, and on how you can change its display yourself.

There are three ways for you to interact with Jmol structures: using the mouse, accessing the menu, or using the Console.

The Mouse: Rotating, Translating, and Zooming

These are basic skills that are essential for getting the most out of Jmol. The links in this section allow you to view each action before trying it with the mouse.

Rotation of molecule

View rotation

To rotate the molecule yourself, left-click and drag on it. Drag the cursor up and down for x-axis rotation, left-right for y-axis rotation.

Translation of molecule

View translation

To translate the molecule yourself, shift-double-click and drag on the structure--the molecule will follow the mouse.

Zooming

View zooming

To zoom the molecule yourself, shift-click and drag. Drag the cursor down to zoom in, up to zoom out.

Jmol Menu Basics

To get started, let's position the structure with the following animation, and think about why we might want to change the display.

The structure at left is a bacterial chlorophyll A protein. From this display, you can see that It is composed of multiple parts. There are two polypeptide chains, displayed as flat ribbons, each in a different color. Each chain (or subunit) also has a non-protein component, displayed in a stick model. These are the pigments that enable chlorophyll A to harvest light energy.

The display as rendered here clearly shows the folding patterns of the polypeptide chains, as well as the bonds of the pigment. However, with this presentation you do not get an accurate picture of the shape of the molecule, nor of the space occupied by the structure as a whole. Let's see how we can change the display to emphasize these different aspects.

[Throughout this section, text in this style indicates selections to make using the Jmol menu. ]

First, access the Jmol menu...
Access the Jmol menu by clicking on the word "Jmol" in the lower right corner of the structure display area. The main panel of the Jmol menu will appear. (To close the menu without using it, click anywhere else in the structure window).

...then Select...
After accessing the main panel of the Jmol menu, move the cursor over the word Select. In the Select submenu that appears, click on All. The whole menu will disappear, and Jmol will perform the task of selecting all the atoms in the structure--but the display will not change (yet).

...then Render.

Access the main menu again. This time, place the cursor over Render to see its sub-menu. In the Render submenu, move the cursor to Atoms and then click on 100% vanderWaals. The menu disappears, and Jmol changes the display so that each atom in the structure is a solid sphere. This rendering is commonly called "spacefill". ("vanderWaals" describes a certain type of spacefill.)

Check your results
In this tutorial, you can check that your menu selections work as expected by clicking the "View Animation" links, which will trigger the display to show what the menu selections should have achieved. Compare your current results with this display:

Here are the same instructions written in a shorthand way:
Select | All
Render | Atoms | 100% vanderWaals
From here on, we'll write all the menu commands in the shorthand style. To return to the original display, here are the commands:
Select | All
Render | Atoms | Off


The Jmol Menu

Removing things from view

What if you only want to see the protein, without the pigments?

The pigments (which are ligands of this protein) were displayed as bonds only, so turning off the bonds turned off the display of the pigments altogether.

Now let's redisplay the pigment, this time as a "ball and stick" model, and also with the atoms colored by element.

Zoom in using the mouse to get a better look at the atoms of the pigments.

Showing specific amino acids:

Sometimes, you may want to look at a certain amino acid or a type of amino acid in a molecule. For example, some proteins are stabilized by disulfide bonds, which are covalent bonds formed between two cysteine side chains. Three disulfide briges are present in the protein insulin. First, we'll look at the overall structure of insulin.

As you see, insulin is quite a small protein. To the see disulfide bonds, use the Jmol menu in the sequence below:

Select | Protein | All
Render | Atoms | Off

(Don't worry, it's supposed to disappear!)
Render | Structures | Cartoon
Select | Protein | By Residue Name | CYS
Render | Bonds | 0.3 Å
Color | Disulfide Bonds | Yellow

Note that that the cartoon and stick renderings would have been hidden by the spacefilled atoms if you had neglected to turn them off. This is because the current rendering choice is not automatically turned off when another choice is selected; each rendering style is controlled individually, so multiple display styles of the same atoms are possible.

You can also change the display of disulfide bonds under Render | Disulfide Bonds, but note that they must be part of the currently selected set of atoms to be affected by the change.

Inverting selection

What if you want to change the display of everything except the cystines?


The Jmol Console

Jmol can also be controlled using a command language. Knowing even a few simple commands can useful. To access the Console, use the Jmol menu:

A small window, the Jmol Console, will appear at the upper left corner of your screen. A cursor will be blinking in the lower part of the window. This is where you can enter commands.

Type the following command:
select all
and click the "Execute" button on the Console. Jmol writes a few things into the upper part of the Console window after executing the command, including the number of atoms selected.

Now type:
color purple
and click the "Execute" button again.

And finally, type:
spacefill 100%
and click "Execute".

The Console allows very powerful control of Jmol with the command language. You can see a listing of Jmol commands at the Jmol interactive scripting documentation page (opens a new window).

Now that you are more familiar with Jmol, click below to move to the section on protein secondary structure.

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For additional information or help with Jmol, see Structure Tutorial Help.


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