If RasMol is not already running, start the program by dragging the file icon of 3b5c.pdb onto the RasMol icon. After the file is loaded, two windows appear. RasMol's Main Window displays a wireframe model of cytochrome b5. Behind the Main Window is the Command Line window, which you use to issue commands to RasMol. (If you are working in Windows, the Command Line window starts out minimized to an icon at the bottom of the screen. If you don't see it, hold down the Alt key while you press the Tab key repeatedly. When the banner says "RasMol Command Line", let up both keys and the Command Line window will open.) When RasMol needs to tell you something, its messages also appear in the Command Line window. When RasMol is waiting for a command, the prompt, "RasMol > " appears on the command line, which is the last line in the window.
Arrange the windows conveniently, as follows:
Windows: Command Line
The Command Line window comes to the front. You can also
accomplish this by simply clicking on any exposed part of the window.
Grab the window, by placing the mouse pointer on its top border and
holding down the mouse key, and drag it to move it. Place it so that
its lower left corner is very close to the lower left corner of the
screen.
< return >
< return >
< return >
Each time you press return, the cursor moves down the window
and prints the prompt, "Rasmol >" on the command line. Keep
pressing return until the prompt appears at the very bottom of
the window. Now use your first command to get a brief introduction to
the program:
RasMol > help < return >
Read the introduction.
RasMol > help commands < return
>
This information includes a list of the most frequently used RasMol
commands. Any time you would like to know more about a command, just
type help followed by the command. This help is somewhat
sketchy compared to the RasMol
Manual, but is quick and handy.
Windows: Main Window
The Main Window returns to the front. You can also accomplish
this by simply clicking on any exposed part of the Main Window. Click
on the small square at the top right of the window. The window
expands to fill the screen. Then drag the small square at the bottom
right of the window straight upward to shrink the window just enough
to expose the last two lines of the Command Line window. With
this arrangement, the Main, or graphics, window is as large as
possible, but you can also see the command line and RasMol's
messages.
In the Main Window, you are now seeing a wireframe model of the protein cytochrome b5, a protein involved in redox reactions in the liver. This small protein contains 86 amino acid residues and a heme prosthetic group with a central iron ion that is the site of oxidation or reduction. The structure you are seeing is the oxidized (Fe3+ or iron [III]) form.
When RasMol starts, it always shows a wireframe model of all the atoms in the protein and in any other molecules (such as cofactors or inhibitors) that are included in the PDB file.
Now you will simplify the display and learn how to manipulate the model.