RasMol

RasMol is a program for viewing three-dimensional structures of molecules and is freely distributed . If you don't have RasMol on your computer, versions for Macintosh Classic, Windows, UNIX, and VAX/VMS can be downloaded from:

http://www.umass.edu/microbio/rasmol/index2.htm

Go to the following link for an enhanced version of RasMol

http://mc2.CChem.Berkeley.EDU/Rasmol/v2.6/

There is no version for Mac OS-X, but the UNIX version may work under Mac's X-Windows. This site also includes information for "configuring Netscape to use RasMol as a viewer/helper application."

RasMol reads special text files containing the positions of all of the atoms in molecule as well as other types of structural information. It then displays a picture of the molecule in any chosen orientation and in a variety of formats. When a molecule structure file is first loaded, it appears in a standard orientation and with a standard format.

Protein and Nucleic Acid Structure Files can be Downloaded from the Protein DataBank

http://www.rcsb.org/pdb/

Here is a useful site for small molecul structures:

http://www.okanagan.bc.ca/chem/molecule/molecule.html

RasMol Reference Card in Acrobat PDF Format

Figure 1 shows the RasMol "Main Window" displaying a piece of DNA in the "Ball and Stick" format; this format mimics a molecular model in which the atoms are represented by different colored balls and the bonds holding the atoms together by sticks.

RasMol allows you to see a molecule in any orientation: In an actual RasMol display, you can change the orientation of the molecule by moving the scroll bars on the right and on the bottom, or you can simply "grab" the molecule with the pointer by holding the mouse button down and "dragging" the molecule into the orientation you want (Note: you cannot change the orientation in these Figures because they are static images and not actual RasMol display windows).

Figure 2 displays the DNA molecule in a different orientation. The orientation was changed by dragging it with the mouse. Note how the positions of the scroll bars have changed. It is very useful to move the molecule around and look at it from all angles.

You can change the display format by clicking on the Display menu and selecting the type of display you wish to see from the pull down menu. In Figure 2, the Display pull down menu is shown with the "Spacefill" option selected. When the mouse button is released, the display will change to that representing a spacefilling molecular model.

Figure 3 displays the DNA molecule as a spacefilling model. This is a format in which each atom is represented by a sphere with a radius large enough to enclose all of the electrons of the atom. In this "cpk" color scheme, each atom is represented by a distinct color; red for oxygen, gray for carbon, magenta for nitrogen, and orange for phosphorous.

You can select different color schemes from the color pull down menu. It is useful to look at a molecule with different display options. The "Ball and Stick" option is most useful since all atoms and chemical bonds are easily seen, but it is misleading in suggesting that the molecule has a lot of open space. The "Spacefill" option shows how much space the molecule really occupies. The "Ribbons" display option is useful in viewing protein structures in which the protein polymer can adopt several different conformations called "secondary structure."

The RasMol Command Line Window is shown beneath the main window and is used to type text commands to RasMol. The text commands can do the same things as the pull down menus and much more. You don't have to worry about the command line window in using Biology Lab Online.