Opening your image on RasWin:
First, make sure you saved your image as Rawdata- text file from Molecules R Us. After sending the image to the zip disk, locate it, right click on it, select "Rename" and name your protein whatever (Hank is nice) followed by .pdb (ex. Hank.pdb). This will change the appearance of the icon. Then click on the icon, hold and drag right on top of the Rasmol/Win icon. The command line is at the tool bar at the bottom of the screen.

Rotating the image:
Click anywhere on the protein with left mouse button. Move the mouse while holding the 'click'.

Centering the image:
Click anywhere on the protein with right mouse button. Move the mouse while holding the 'click'. At the prompt, you can also type
>>Reset

Zooming in/out:
Click on the protein with the left mouse button. Holding the "Shift" key, move the mouse UP to Zoom in, Down to Zoom out.

Selecting every amino acid of a particular type (ex, all serines):
>>select ser
This works except for cysteine. To select all cysteines involved in a disulfide bond (cystine):
>>select cys
To only select free cysteines:
>>select cys and not cystine

Selecting an entire chain:
Clicking on the molecule will tell you what chain you have clicked on. To select Chain A for example:
>>select :a

Selecting a particular amino acid (ex, all leucines) in a chain:
>>Select leu:e this selects all leucines in chain e.

Selecting a particular residue in a particular chain:
Example serine 276 in chain f.
>>Select ser276:f

Selecting an individual atom:
Click on which atom that you think you might want to label, such as one involved directly in a DNA protein interaction, for example. The command screen will tell you what type of atom you picked (O for oxygen, N for nitrogen, C for carbon), the position on the amino acid or DNA molecule (such as A for alpha carbon: would look like "CA") and the atom number itself. In order to highlight that particular atom:
>>select atomno=2061
then you may want to color it:
>>color magenta
Only that atom in the residue or molecule will be highlighted that color.

To select an entire nucleotide:
Click on the nucleotide. The command will read the type of atom, position, and atom number first, which may be handy to know. Next in line it will say Group: and what ever type of nucleotide base such as A, C, G, T and a number (don’t ask me what the number is, but it’s useful). To select that residue, say T 33 (base and number):
>>select T33
That entire base should be ready for color, structure changes (spacefill, ball and stick, etc. under menu "display").

Finding the distance between two atoms:
>>Set picking distance
Now click on two atoms. The distance should appear on the command screen. To turn this function off:
>>set picking ident

To show a bond and bond length between two atoms:
>>Set picking monitor
Now click on the two atoms again. A bond line should appear. By clicking on the atoms more than once, the bond will be erased.
To turn off the "picking monitor" function
>>Set picking ident
Now you can resume clicking happily on any atoms you please without disrupting your image with messy bonds.

Making Your DNA Look Cool:
This is my favorite. I stole it from an interactive instructional manual on the web. I like to call it: Making Your DNA Look Cool.
>>select DNA
>>color white
or what ever color you want it to be
>>spacefill
>>center selected
>>select DNA and backbone
>>color cyan
or what ever color you want it to be
>>select within(3.1, DNA) and not DNA
Because a typical H bond length is under 3.1 Angstroms, this selects H bonds between the DNA and protein, but specifically on the protein side. The "and not DNA" part makes sure you don’t select bonds between DNA atoms. That would be sloppy.
Now, press the UP arrow on your keyboard to retrieve the command "select within(3.1, DNA) and not DNA" and add on to the end of it "and not water" so your command line will look like this:
>>select within(3.1, DNA) and not DNA and not water
This selects water present in the crystal within 3.1 Å of the DNA and H bonding with in 3.1 angstroms, I think. This addition, if you color it, will change the color of your bonding atoms on the protein side, if there is no water. To specifically show the atoms in the DNA molecule that are bonding with the protein:
>>select within(3.1, protein) and DNA, color cpk
This labels all the DNA-protein bonding atoms on the DNA side, in their standard colors, whatever they are. Because I don’t know an undo command, don’t do this if you think the primary cpk colors will look junky.

Other Tricks:
Here’s some other cop out tricks since I don’t know any better commands:
If you want to Hide a portion of your structure, I like to select the residues or chain and color it the same color as the background then make it wireframe.
>>select :b or >>select 165-232:b
>>color black
>>wireframe
This way when you want to do close up imaging, pesky residues won’t restrict you view as much. There is also a command called restrict, but if you can figure it out to work for hiding parts of the structure, then you are the RasMol King or Queen. I also like to highlight residues by selecting an entire or portion of a chain to backbone then turning the residue I want to enforce into a ball and stick structure: ex
>>select 142-155:g
This selected residues 142-155 in chain g. Then go to the menu bar and click "display" and select "backbone". You can then color it if you want. White backbone on a white background looks real nifty. A shadow is cast just enough that you can still make out the backbone. Anyway, to then highlight your residue of choice, alanine 144 for example in the chain that you just "backboned":
>>select ala144:g
Then go to the menu bar, click on display and select ball and stick. This technique also looks pretty neat with the ribbon structure. Then, show bond lengths by clicking on one of the balls. Between protein and DNA, for example, you would find bonding between H-N, H-O, N-O, so it's pretty easy to determine what's bonding where just by clicking on atoms (bond length, remember, is within 3.1). Selecting residues in sequence such as selecting residues 142-155 can also be used if you want to demonstrate termination points of alpha helixes and beta sheets. Remember, which residue is a helix breaker? Proline!

Saving the image:
In order to properly save your image, don’t do what Dr. Lee says on the Protein Structure Project link on his web page. It is correct, but the protocol is slightly more involved. You could misplace a real cool image that you spent hours on if you assume that it will be saved on your disk. Here is what you really do:
>>write imagename.gif
Use this for Raswin. For Rasmol, leave off the ".gif" part. Please folks, substitute a real name for your image; ex. your image is a close up of cyclic AMP interacting with DNA, you may want to type at the prompt: >>write campdna.gif . Name your images different things also (see warning on Dr. Lee's Protein Structure Project link). You typed in your image name at the prompt as done above and pretty much it appears that nothing has happened. The image isn't on your disk, it's saved to the C: drive. You can retrieve it using the "find" function by clicking on Start on the Windows tool bar and you'll see "Find" with a little magnifying glass icon. Select "Files or Folders". Type in your image name (ex. campdna.gif) in the "Named" box under the Names and Locations tab. Make sure location is the C drive. Once you image is found you can right click on it, select "Send To" then select whatever drive is the zip drive. Sorry Mac people, I'm not sure what the protocol is for that. So have him go over it extensively in class. What the heck, you probably wouldn't pay attention anyway, so, drop in at his office hours and make him take you the computer lab so you can do some practice runs.