RasMol Start

What do I need to know first?

Rasmol was developed by Roger Sayle as a research tool for viewing large molecules. In order to get the most out of Rasmol's many useful and powerful funtions, you need to know some basic chemistry. For starters, you should be familiar with the notation and some of the properties of commonly encountered elements such as carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P), sulfur (S), and so forth. You also need to be aware of the different kinds of chemical bonds and how they affect molecular structure, in particular, covalent bonds between non-metal atoms and intra-molecular hydrogen bonds. For larger molecules (proteins) you need to understand the concepts of hydrophilic and hydrophobic regions. 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 browser.

The main purpose of this RasMol tutorial is to guide you through the process of downloading, installing, and using RasMol. As you go through it, you will be directed to click on hyperlinks that will give you detailed instructions each step of the way.

Why would I want to use RasMol?

If you're unsure, take a look at the gallery of images. Imagine being able to generate such images of your favorite molecules, and then rotate them, or view them in stereo, in order to comprehend their 3-D 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.

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. Choose the system you want to download Rasmol to:

PC with Windows 98 or 95 (Note that for PC using Windows 98 or 95, the program is called RasWin).
Macintosh
Other

Note that version 2.6 beta 2a is recommended for use with this tutorial. It would be best to avoid Berkeley-enhanced RasMol version (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. There are several kinds of atomic coordinate files that Rasmol can use, but the most common are the Protein Data Base (PDB) files. You can get some sample PDB files by clicking here. These files can be put in the same folder/directory as the RasMol program, or elsewhere on your hard disk. After you have started up RasMol, click on the File, Open, menu, and choose a molecule to display.

OK, I see the molecule. Now what?

Try out RasMol's menus. 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. You can also use the command-line window. In addition to the black window, RasMol has a second, white, window called the Command-Line Window. 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 on the 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. 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. Then type "color cpk" to restore the default color scheme. 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?

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.

I've made it this far, how can I find out what else can I learn about a protein/DNA molecule with RasMol?

Click on one of the class specific tutorial pages to learn about some of the advanced options Rasmol offers. You can also learn about some of the powerful RasMol commands in more detail at the following resources:
Umass Rasmol and chime page. This is one of the largest and most extensive sites with several tutorials and links to many other sites. 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!).




This site was created by Robert Findley and Daryl Findley. Send questions, comments, and problems to [email protected].
Inspiration and information were borrowed in part from the excellent Rasmol and Chime site by Eric Martz from umass.