JSmol and Jmol: molecular graphics viewers

Written by Helen White; updated by Nick Keep and Clare Sansom

Introduction

Proteins, by their nature, have complex 3D structures which cannot always be easily appreciated from a 2D picture. A far better way of getting a feel and understanding of a protein's structure is to manipulate it interactively using a molecular graphics program.

The principal program that we will be using throughout the PPS course is JSmol which is freely available. It is the lastest variant of a Java-based program called Jmol which avoids the need for Java when displaying structures embedded in webpages. Jmol, in turn, is descended from RasMol, which was written in the 90's and was the first program to make fast molecular graphics of complex proteins available on ordinary desktop machines. Like Rasmol, Jmol and JSmol allow users to rotate protein structures, zoom in on them, render them in different ways and using various colouring schemes, label atoms and residues, and so on, as well as exporting images of structures in a number of graphical formats.

JSmol should work for the images that are embedded within our web pages on most browsers and platforms including on Android and iPbone/iPad. However, if you want to make your own images you will have to install Jmol on your own computer.

The rest of this page gives you instructions for installing Jmol on your computer. You will need to use it (sometimes another graphics program of at least equal capacity will do) to answer some of the courseswork questions and in your project work.

Getting Jmol

Installing Jmol on your computer

Jmol can be obtained from the following link to the Jmol website. In the heading, you will find a number of options, including Download. Click on this to go to the Jmol download page where the link to download the latest version of Jmol can be found.

An extensive operating manual can be found by clicking on the documentation and demonstration pages links found on the Jmol home page. Instructions can also be found under the help when you are running the program. You may also want to do a Browser Check (found as a link on the top of the Jmol homepage).

To help familarise you with this program, we will go through a few basic commands. You should note that both JSmol and Rasmol work in very similar ways.

Using Jmol

Reading in the coordinates
The following link contains the 3D coordinates of a protein structure (in PDB format).

PDB file

Handy hint:

To download the above file don't just click on the above link. Press the SHIFT key down and then click on the link. You will then get the usual dialogue box asking where to save the file. Under Windows you may need to right-click on the link.

The protein, in case you're interested, is the SH2 domain of a tyrosine kinase and consists of two chains and a bound ligand (search for 1a07 in the PDBsum database).

Once you have the coordinates on your disk, Jmol can be started. Once the Jmol window is on your screen click on the File button on the toolbar and you will see a number of options:

New - allows you to open a new window
Open - allows you to search for the directory where you have your pdb file, and then click on it to read it in. This can also be done by clicking on the first icon underneath the tool bar
Open URL - allows you to read a pdb file directly from a URL
Export - allows you to export your picture to JPG, PNG or PPM format
Script - opens a window where you can use RasMol commands to give a more specialised selection of atoms, residues or chains than with the mouse
You can also print, close and exit the program.

Read in the pdb file you have downloaded (use the option "Open" mentioned above) and investigate what you can do with the mouse.

the left hand button will let you rotate your molecule
the middle button will let you zoom in and out
the right hand button will bring up viewing commands

Now investigate some different methods of displaying the molecule. Note: During the course you will find may Jmols incoporated within the text. You can use the right hand mose button and the commands below to manipulate them.

Click on the right hand mouse button and a menu will come up, go down to Style, slide the mouse across to Scheme, and then across to CPK Spacefill. Repeat the process but try the other options for display i.e. Ball and Stick, Sticks, Wireframe. You should obtain pictures like those in Figure 1.

Figure 1: 1A07 displayed using CPK spacefill (left) and wireframe (right)
For the rest of the time the above commands will be shown in the form Style - Scheme - CPK Spacefill.

Sometimes we do not want to look at all the atoms, for instance we may want to see the secondary structural elements in more detail.

Click on the right hand mouse button, go down to Style, then down to Structures. Try to display the molecule using Trace.
This will display on top of your atoms and bonds, so you will have to switch them off. This is done Style - Atoms - Off and Style - Bonds - Off.
A similar scheme may be used to show the molecules as a Cartoon or Ribbons. However, you will have to do Style - Structures -Off to erase the Trace display otherwise both Trace and Ribbons will be displayed on top of each other.

So far the pictures have been very dull, but we can add colour to illustrate different aspects. One common method of display is by viewing the secondary structural elements, where the default colours are red for helices, yellow for beta-strands and white for the rest. We can do this easily in Jmol.

Load in you pdb file as previously
Do the commands Style - Structure - Cartoons
Switch off the atoms and bonds as previously.
Use the right hand mouse button and go down the menu until you reach Colour. Then select Cartoons. In the third column that appears choose By Scheme. This will then bring up the possible colour schemes. Amino will colour by amino acid, so that you will end up with a multi-colour display. Secondary Structure will colour by helix and sheet, while chain will colour by chain. This is very useful when a protein consists of more than one chain.

Figure 2: 1A07 represented as a cartoon, coloured by secondary structure(left) and chain (right)
These colour schemes can also be used in the display of atoms and bonds. Now try

Style - Atoms - 15% vander Waals
Style - Bonds - On

Colour - Atoms . You can try By scheme or by the different colours. If you choose to colour Yellow for instance, you will have to select the shade of yellow you want from the fourth column.

So far we have looked at a complete molecule, but we are also able to display specific items. Try the following:

Open your pdb file file - open then give filename
use the right hand mouse button to obtain a menu
Style - Scheme - Wire Frame
Colour atoms - White.

We are now going to colour specific types of residues.

use the right hand mouse button to obtain a menu
Select - Protein - Basic Residues (+)
Colour - Atoms - By Scheme - Amino.

This will display the positively charged residues in blue

Select - Protein - Acidic Residues (-)
Colour - Atoms - By Scheme - Amino.

An interesting display can be made of the whole molecule coloured by atom, using CPK.

This is achieved by

Select - All
Style - Scheme - CPK spacefill

If you follow the above scheme, you should obtain the picture shown in Figure 3.

Figure 3: A Spacefilled representation of 1A07. The positively charged residues are coloured blue, the negatively charged residues are red. All other residues are white.

You may be interested where all Tryptophan side chains are located. This is simple to achieve. A possible example can be obtained as follows:

Open your pdb file file - open then give filename
Display your molecule as a backbone or trace (Style - Structures - Backbone or Trace.
Select the residue you are interested in (Select - Protein - By Residue Name -TRP)
You can colour the atoms (Colour - Atoms, then choose By scheme or a specific colour)

Style - Scheme followed by one of the choices e.g. sticks
Style - Atoms then choose a vanderwaals radii. Also Style - Bonds and choose a width
You can also have the atoms switched off and just display the bonds (Style - Bonds) then choose a width

Many pdb files, such as 1A07.pdb have water atoms and/or ligands. Jmol also allows us to manipulate these. Try the following:

Open your pdb file file - open then give the filename
Select - Protein -All
Style - Structures - Trace
Style - Atoms - Off
Style - Bonds - Off
We are now going to manipulate these "hetero" atoms
Select -Hetero -Water will select only the water atoms, so the program will apply all future commands only to these atoms.
Colour - Atoms - Yellow -Yellow should change all the water molecules to yellow, as shown in the next picture

Style - Atoms -Off will switch off all the water molecules

There are more menu options available which you should try

label - where you will find different label types and positions
Hint: If you leave the cursor on an atom for a few seconds, the atom label will show.
spin - you can vary the spin rates in each direction
In the colour option you can select background to change the background colour. Of course, if you change the background colour, you may have to change some of the colours that you used in your molecule in order to give a good contrast.

If you return to the Jmol website and click on the Demonstation pages to see further capabilities of the program. Wikipedia also has links to other sites featurng Jmol explantaions.

Note that although (almost) all the examples in this course use JSmol, you are not obliged to use it or Jmol. You may want to use the predecessor program, Rasmol, which is also freely available. We discuss some more complex molecular graphics and modelling programs later in the course; if you want to get ahead, you can start with this post on the PPS blog.

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