RasMol Tutorial for Viewing DNA

What is RasMol? What can it do?

RasMol is a program that view PDB files. PDB is a file format used for large molecules such as protein or DNA These files can be found on the web in Brookhaven protein data bank or created using other programs, such as Spartan. RasMol can be used to rotate the molecule, change mold type it is viewed in, and color the molecule. Specific residues can be identified, as well as different structures. RasMol can only look at one PDB file at a time. RasMol images can be saved in different picture formats for display on the web or within a word document. RasMol is "freeware", which means you can install in anywhere for free.

RasMol Resources

RasMol Home Page

http://www.mtholyoke.edu/~emlaughl/rasmol/raspro.htm

RasMol on your desktop

See the attached instructions, "How to use RasMol from any Mac..." or "How to get RasMol on PC...", if RasMol is not already on your computer.

Getting DNA Structure

Open up Netscape and go to http://heme.Gsu.EDU/glactone/PDB/DNA_RNA/dna.html

Scroll down to the bottom of the page.

Click on the one of the forms of DNA

Click on Pick app

NOTE: On other versions of Netscape, when you click on the DNA link it may open a window within Netscape. To get the PDB file, go under file and Save on the desktop.

Open up the RasMol folder on the desk top and select RasMol

Click on Open

*You will only have to select the application the first time you open it.

It should look something like this:

To rotate the DNA click inside the main window and hold, while you move the mouse.

RasMol has two windows: one is the main window that displays the image and the other is the command line window. The command line window allows the user to enter commands. Many of the commands can also be accessed in a user friendly manner by using the menu options at the top of the screen. However, there are commands that can only be done by typing in the command. This next section will show you a few of each type of commands relevant to viewing DNA.

Under the Display Menu select Backbone

Also try Spacefill under the Display options. Coloring

RasMol allows you to color specific groups. In proteins you can color specific amino acids and in DNA you can color specific baces.

Return to the wireframe mode by going to Display again and selecting wireframe.

Try the following list of command by typing them in the command window. Watch the image after each color command.

Clicking for Identification

Click on part of the DNA

The name a location of the group you clicked on should show up in the command window.

You should get something like this:

Atom: H8 191 Group: A 6 Chain: A

(In this case I clicked on a Hydrogen (H8) in an Adenine (group A), and on chain A.)

Now view the structures of the other two forms of DNA, by repeating these instructions.

NOTE: Sometimes RasMol does not automatically open the main and command window, so it will look like it isn't working. Make sure you are in RasMol, go to Window on the menu bar and select Main and you will see the image. To get the command window, select Command line from the Window menu.

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http://www.mtholyoke.edu/~emlaughl/rasmol/rasdna.htm

written by: Elsa Laughlin 2/9/98