RasMol Quick Start

by Eric Martz, December 1996 (minor updates December 1998)

What do I need to know first?

2H2O showing one hydrogen bond
In order to understand what Roger Sayle's wonderful program RasMol can show you, you need to know some basic chemistry. You need to know about elements such as C, H, O, N, P, S, and so forth. You need to know about covalent chemical bonds, and noncovalent bonds such as hydrogen bonds. For larger molecules (proteins) you need to understand the concepts of hydrophilic and hydrophobic. If you need to learn more about these subjects, consult a chemistry textbook, or a biology textbook which includes a good section on chemistry and biochemistry.

You will also need to know how to use your computer, or have help from someone who does. You will of course need to know how to use your web browser, and how to download files with your web browser.

The main purpose of RasMol Quick Start is to guide you through the large number of pages at the RasMol Classic Main Page. Therefore, RasMol Quick Start is not complete by itself. As you go through it, you will be directed to other sections of the RasMol Classic Main Page by hyperlinks (usually colored blue and underlined). You will have to read certain of these additional linked documents carefully and follow instructions.

Do I want to use RasMol?

If you're unsure, take a look at the
gallery. Imagine being able to generate such images of your favorite molecules, and then rotate them, or view them in stereo, to comprehend their 3D structure! RasMol allows you to explore the structure of a molecule by "getting into it and climbing around". RasMol works well both for small organic molecules and for large ones, such as proteins, DNA, and RNA.

Wow! Let's get started!

Where do I get RasMol, and how do I install it?

You need to select the version of RasMol which is best for your computer. All available versions and instructions for installation are accessed through the page Getting and Installing RasMol.

At the outset, it would be best to avoid Berkeley-enhanced RasMol (UCB-RasMol). This derivative of RasMol has a number of bugs and will not run many existing scripts. After you have some experience with RasMol, try it if you are interested in moving molecules relative to each other.

OK, we'll assume you now have RasMol installed. When you click on RasMol's triangular 3-atom icon to run it, a black window titled 'RasMol' should appear.

OK, I see the black window. What do I do now?

Get some molecules to look at.

In order to view a molecule in RasMol, you need a separate file which specifies the structure of the molecule. This is called an atomic coordinate file. My own favorite starter molecules are ATP for a small/micro molecule (file atp.pdb) or, for a macromolecule, a transcriptional regulatory protein from yeast (gal4) bound to a short segment of DNA (file 1d66.pdb). Other good ones are the oxygenated form of human hemoglobin (1hho.pdb) and a section of a theoretically modeled lipid bilayer containing an ion-permeable gramicidin channel (bilagram.pdb). (More information is available about hemoglobin or about lipid bilayers, including a movie script on the latter.)

You can get these 4 molecules packaged into a self-unzipping DOS file named fourmols.exe for Windows computers, or separately for Macintosh or unix computers. (Shift-click to download PDB files directly.)

These files can be put in the same folder/directory as the RasMol program, or elsewhere on your hard disk. Use RasMol's File, Open menu to find and display a molecule.

OK, I see the molecule. Now what?

Try out RasMol's menus

This is a "snapshot" which can't be moved. You must run RasMol to move the image with your mouse.
Hold down the left mouse button and move the molecule! Remember to do this often. (Here is the complete set of mouse controls.)

Notice the pull-down menus in RasMol, such as Display and Colours. Try different representations from the Display menu. Only wireframe, sticks, and ball and stick apply to small molecules. If you are looking at a protein or DNA, try color schemes other than the default CPK (Corey, Pauling, Koltun).

Cool! But how do I find out what I'm looking at?

First, use the File, Information menu. This will often tell you what molecule you are looking at.

Use the command-line window

This is a good way to arrange the two windows. Make sure you have the bottom of the white window in view, since this is where the action occurs.
In addition to the black window, RasMol has a second window called the Command-Line Window. It is white. If you are working on unix or a Macintosh, it may be behind the black window. If you are working in Windows, the white window starts out minimized to an icon at the bottom of the screen. If you don't see it, look for it on the Win95/NT taskbar. There will be two items on the taskbar, one labeled "RasMol version 2.6" and the other, "RasMol Command Line". Click on the latter to open the white command line window. Only the former has the 3-ball icon. (If you are using Windows 3.1, hold down the Alt key while you press the Tab key repeatedly. When the banner says "RasMol Command Line", let up both keys and the white window will open.)

Move or resize the black and white windows so you can see both windows at once. Now, click on an atom, and RasMol will identify it in the white window. For example, if you click on the topmost atom in the initial view of 1D66.PDB, RasMol reports

Atom: NZ 1446  Group: LYS 33  Chain: B

The first letter, N, identifies the atom as nitrogen. The second letter, Z, indicates that the N is in the zeta (6th) position from the alpha carbon, CA. This atom is number 1,446 in the total of 1,707 in this structure. This N atom is part of a lysine amino acid, which is residue number 33 in chain B.

The command-line window can also accept commands which you type. For example, type color green and press Enter/Return. The molecule should turn green. This is a trivial example, but RasMol has an extensive and powerful command language which goes far beyond what you can do with its pull-down menus.

How do I figure out what I've got in a macromolecule?

Transcriptional regulatory protein bound to DNA
With proteins or DNA, after you first open the molecule, use the Display menu to select Backbone, and then the Colours menu to select Chain. Now you can see how many amino acid or nucleotide chains are present, since each has a different color.

To find out whether anything else besides protein and dna is present, type the command select not (protein or dna) including the parentheses and press Enter/Return. For 1D66, 55 atoms are selected; for 1CRN, none. If some atoms were selected, use the Display menu to select Spacefill to show only the selected atoms. Usually most of them are the oxygens from water molecules. (The hydrogens are not resolved by the method most often used to structure proteins, X-ray crystallography.)

To find out if anything other than protein, dna, or water is present, type the command restrict not water. If anything remains, click on it to find out what it is. In the case of 1D66, 4 cadmium ions remain.

If you got this far, next have a look at What can you learn about a protein/DNA molecule with RasMol? which explains some powerful RasMol commands in more detail.

Well, we've given you a quick start with RasMol. To find out more about RasMol, here are the resources you'll need.

Molecules Galore!

The Molecules Galore page tells you where to find over 1,000 micromolecules and several thousand macromolecules on the web.

Do some RasMol Tutorials

There are Tutorials on How to Use RasMol.

Use the RasMol Reference Manual

An up-to-date version of the RasMol Reference Manual is available in hypertext. Check out the other supplementary documents.

Get the built-in help.

Built-in help can be accessed from the Help Menu of RasMol, or by typing 'help' in the command-line window (which is explained below). However, in order to work, two files must be present in the same folder/directory as the RasMol program. All versions require the file RASMOL.HLP, which supplies the command-line help. Windows versions also require the file RASWIN.HLP, which supplies information for the help menu. (The help menu is absent in the Macintosh version.)

The files RASMOL.HLP and RASWIN.HLP are available packed into a self-unzipping DOS file RASHELP.EXE for Windows computers. RASMOL.HLP can be downloaded for Macintosh computers (hold down Shift before clicking to force saving the file, and use BINARY mode!).

Explore the RasMol Classic Main Page!

There's lots more to be found at the RasMol Classic Main Page!