HOW TO GET AND USE RASMOL

RASMOL is a public domain program that can be used to view molecular structures in 3-D perspective. It is an easy program to use. It does have research applications, and can be used to view the structure of macro-molecules like proteins. We shall be using this program to understand basic molecular structure principles. This handout describes how to get RASMOL, and how to use it.

Step 1 - Get The Software. Use an Internet browser, such as Netscape, to open the online version of this document.  Go to the course Home Page, click on Software Downloads, click on RASMOL.  Then Click on the DOWNLOAD LINK.  Notice (or set) where the file "RASMOL.EXE" gets saved. Then click OK. What you get is a "self exploding" compressed file. The compressed file includes two versions of the actual program, some help and documentation files, and a number of *.pdb molecular structure data files.

Step 2 - Install the Software. On your own PC, use My Computer to locate RASMOL.EXE. Double-left-click on the file name. Edit the "Extract To:" window to specify some NEW folder/directory, such as C:\Programs\Rasmol. Click "Extract" and then Click "Yes". Warning: It's an old program that can't handle long folder names. Don't, for instance, extract this to "Program Files" or any folder with a more than 8 character name. All the files will be placed into the new folder. Still using My Computer, open a window to the RASMOL folder. Right-Click on RWIN32B2.EXE, left click on Send To..., Desktop (create shortcut), OK . This will create a icon/shortcut to the program. Right click the icon, select Properties and click the tab "Shortcut." Under "Run" select "Maximized" and then click OK. Rename the icon as "RASMOL." ( The RWIN16B2.EXE version is there for antique computers using Windows 3.1.)

Step 3 - Open and Learn to Use the Program. It's easy!
(a) Basic Commands: Double click the icon to open the program.
· Click File, Open, select (click) any file (as C2H5OH.pdb), click OK.
· Click Display, Ball & Stick (or Spacefill, your choice)
· Left-Click-Drag across the top of the molecule to ROTATE it. Alternately, you can drag one of the slide bars. Try clicking and holding down one of the arrows!
(b) Intermediate level commands (optional):
 · Right-Click-Drag to move (TRANSLATE) the molecule.
 · Shift-Left-Click-Drag (slowly, top to bottom) to ZOOM (enlarge) it.
 · Shift-Right-Click-Drag (slowly, left to right) to Z-ROTATE it.

  • You must click on File Close before you File Open another molecule.

    • (c) Obtaining Printer Output: There are 3 basic ways to obtain output. First, however, type "background white". You won't see anything as you type, but when you press Enter, the screen will go white. If not, you misspelled something. Try again. You may try other basic colors as red, green, blue, yellow, cyan, magenta, orange, or violet. White, however, will save you a lot of printer toner/ink.
    · File, Print, OK will print the RASMOL window directly to an attached printer.
    · Edit, Copy will put the RASMOL image into the "clipboard."
    · Alternately, use the RASMOL Export command to write a graphics file. The GIF and BMP formats can be opened and used with many programs.

    Step 4 - Your Homework 6.5 Assignment. Load the molecule of your choosing (but one with at least 5 atoms). Position this "nicely" and Edit, Copy the picture. Next, open the word processor or graphics program of your choice. Edit, Paste the image into a document. Indicate the Name and Molecular Formula of your molecule. Add your own name and the date. Do this with your word processor, not by hand or with an (ugh) typewriter. Print out the result. Turn it in Friday, Feb.28.  An easy 5 point assignment!

    Step 5 - Configure your Internet Browser. Officially, you need to install RASMOL as a helper application. Click on this link: CH4. Click "Pick App", click "Browse", click around to find the RASMOL folder, click on the program itself (RWIN32B2.EXE), click "Open", deslect "Always Ask", select "Open It", and Click OK. Now, when you encounter and click on another  link to a RASMOL data file (*.pdb), RASMOL will open and automatically display the file. As a test, check out the RASMOL TEST PAGE.  Click on some of the links and see what you get. When you close RASMOL, you go back to your browser.

    HAVE FUN !!

    P. S. - RASMOL was authored and made freely available by Roger A. Sayle, a biochemist. That "pdb" file extension is short for "protein data base." Molecular structure considerations are paramount to understanding biochemical phenomena.

    P. P. S. Once RASMOL is installed, you no longer need to save RASMOL.EXE. Delete it, or give it to a friend! Thanks to Michael Shepard for creating this file!

    Comments, Corrections, Questions: E-Mail Dr. Myers