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). These coordinates are the same as those used in the RasMol example.

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:

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


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.


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.

secs 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
So far we have looked at a complete molecule, but we are also able to display specific items. Try the following: If you follow the above scheme, you should obtain the picture shown in Figure 3.

charge

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:

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

There are more menu options available which you should try

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.


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