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Rasmol Help

Alongside all the course material, you are provided with a collection of PDB files which are a way to present molecules using RasMol. RasMol displays molecules interactively in 3D. V2.6 Molecular Visualisation Program . RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and the generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems.

How to obtain RasMol

RasMol is freely available. You can download it from several sources, including the RasMol Homepage where you will find a detailed tutorial of the software.

MBN is distributed with a version of Rasmol. You can find a set up program for it on the CD-ROM.

More on Rasmol

A copy of RasMol (Win 32 version for Win 95)is also provided on the CD Rom of "The Molecular Biology Notebook" and has been installed on your machine.

Basic RasMol Tutorial

To find help: select the Rasmol menu option: Help|User Manual

Description of the package
When RasMol is launched, two windows are opened. A main window contains the graphical interface where you can see the molecule and move it. It also has a menu which offers a shortcut to some of the basic commands. The other window is a command line interface where you can enter some more complex commands, and which also displays some information taken from the molecule you have loaded.
Loading a molecule

If you launched RasMol from your Browser, there should be a molecule already in it. If not, click on Open, and navigate to the folder in your machine where all the molecules are.

Basic mouse functions
- If you click on the molecule and move the mouse, the molecule will rotate in 3 dimensions on your screen
- If you right click and move the mouse, the molecule will move without rotating (translation).
- If you press the Shift key while holding the left mouse button, and move the mouse, RasMol will zoom in or out of the molecule.
Basic Menu function
The menu functions alter the display of the molecule and also can help you save a particular image in different formats.

Introduction to menu driven commands

It is convenient to set up your screen so that you can see both the RasMol main window, and the RasMol Command window. Note than when the RasMol main window is on view, it is still possible to type commands in the RasMol command window. This can be very useful.

Example of useful commands: Load the protein haemoglobin as an example:

Name of the command	Simple description	Try this
Backbone	Show the backbone of a protein	`backbone on; backbone 20; backbone 100 backbone off`
Color	Change the colour of an element to the selected colour. Colours can be designated by their names or by the triplet of their RGB value [nnn,nnn,nnn].	`color backbone red; color backbone [000,255,255]`
Dots	Show the Clouds of electrons as dots around the nucleus	`dots dots off`
Restrict	Will restrict the display of the molecule to the area mentioned: affect wireframe and backbone.	`restrict 1-100:c`
Select	Select a group of amino acids. Most of the commands typed after that will only affect that part	`select heme color red select all backbone color backbone purple backbone 200 select 1-40:a color red select 50-150:b color blue`
Spacefill	Display a spacefill representation of the molecule. Note you can obtain the same effect with the command Wireframe 50	`spacefill spacefill off`
Wireframe	Show the wireframe of the molecule	`wireframe on wireframe 20 wireframe 50 wireframe off`
Zap	Close the molecule	`zap`

An advanced tutorial is available at the RasMol site.

A note on Scripts: It is possible to build a movie that RasMol can display. Please refer to the Homepage of RasMol to download these.