presents
(Revised August 28, 1999—no longer maintained.)
Note added 2008-10-06:
Command structure of RasMol is similar to the much newer Java applet called JMol. This tutorial might be helpful in learning command-line language for complex selecting and coloring, which ain't easy, with JMol.)
If you are really serious about molecular modeling, learn DeepView.
Gale Rhodes
Contact Information
My students tested this tutorial, and as a result, I made many improvements. In particular, I believe that the assignments are now clearer. Thanks to the 1997 biochemistry class, and to Spencer Anthony-Cahill of Western Washington University and Cygnus X-1, for helping to improve this tutorial.
NOTE: Accessory pages like Special Instructions appear in a new browser window; simply close the window to return to this tutorial.
This tutorial gives you an opportunity to learn how to explore the structure and action of biomolecules using computer graphics. You will learn how to obtain macromolecular structure files from the Protein Data Bank, and to display and manipulate molecular structures using the program RasMol. With the skills you learn here, you can independently examine any macromolecular structure available. Many structural biology sites on the World Wide Web provide structures, illustrations, and even animations that you can view with RasMol. You can obtain RasMol free for use on your own computer. See Getting RasMol if you do not already have RasMol installed on your computer (but first read below about Conventions used in the instructions of this tutorial).
RasMol for the Macintosh is called RasMac, but I refer to the program as RasMol throughout the tutorial. I wrote the tutorial using RasMac 2.6b2 for Macintosh. Most of the instructions should be the same for Windows versions of RasMol. Where I am aware of differences between Mac and PC versions of the program, I added notes in parentheses for PC users.
A new version, 2.7.1, is now available in 8-bit and 32-bit versions. For faster display operation on Macs and PCs, get the 8-bit version, and use it with your monitor set to 256 colors. Most of the changes between versions 2.6b2 and 2.7.1 do no affect the operations described in this tutorial.
The name RasMol comes from raster display of molecules. Raster is a type of computer display especially useful for showing solid surfaces. It may not be a coincidence that the letters Ras are also the initials of RasMol's creator, Roger A. Sayle of Glaxo Corporation and the University of Edinburgh, Scotland. Sayle began developing this program as part of this graduate work in computer science, and continues to expand it with support from Glaxo. Thanks to Roger A. Sayle and Glaxo for giving this powerful tool to the world structural biology community.
Conventions
In this tutorial, instructions for giving commands or using
menus will appear in a consistent format. Here are some sample
instructions and their meanings:
< return > (a keyboard entry)
This instruction means press the key labeled return on the
computer keyboard. All key-press instructions are surrounded by <
>'s. When the names of keys appear in descriptive text, they are
underlined, as in the first sentence of this paragraph.
Display: Backbone (a menu command)
means pull down the Display menu and select Backbone.
All menu instructions are in bold type with a colon between
menu name and command name.
RasMol > select alpha < return >
(a command on RasMol Command Line)
means that you should type the command "select alpha" and then press
the return key. Any words that you type while RasMol is running
appear in the Command Line window beside the RasMol prompt:
"RasMol >." When you type the command and press return, RasMol
executes the command.
button: Open (an operation on a dialog
window)
means that you should click once on the button labeled
Open.
link: Other Sites of Interest (on web
pages)
means that you should find and click the link, usually a word
or phrase in colored text and underlined, that says, "Other Sites
of Interest".
Filenames are in boldface -- for example, 3b5c.pdb.
Cytochrome B5 (PDB 3b5c), convergent stereo pair rendered with RasMol. Image exported as GIF file.