2H2O showing one hydrogen bond
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.
Wow! Let's get started!
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).
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?
|This is a "snapshot" which can't be moved. You must run RasMol to move the image with your mouse.|
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.
|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.|
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.
Transcriptional regulatory protein bound to DNA
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.
Well, we've given you a quick start with RasMol. To find out more about RasMol, here are the resources you'll need.
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!).