Display: Backbone
Now you see only the alpha carbons of the protein, connected by
straight lines. Lines connecting alpha carbons are sometimes called
"virtual bonds." You can begin to see secondary structural elements
such as alpha helices and strands of beta pleated sheet. Try some of
the other Display commands. Each command in the Display menu changes
the way RasMol represents, or "renders", the model. End by displaying
the backbone model. Now you will make the secondary structural
features even more obvious.
Colours: Structure
This command colors alpha helices hot pink, beta strands yellow,
beta turns blue, and other parts of the model light gray (not
my choice of colors!).
RasMol > select hetero and not hoh <
return >
This command selects only the hetero (non-protein) groups in the
file, excluding the water molecules that are frequently included in
crystallographic models. Nothing happens until you issue another
command. NOTE that commands affect only the currently selected
atoms. Also notice that you do not need to bring the Command Line
window to the front in order to type commands.
Display: Ball & Stick
RasMol displays a ball-and-stick model of the selected atoms.
Notice that this command does not affect the protein chain, because
it is not selected.
Colours: CPK
RasMol colors the selected atoms according to widely used
chemical conventions: carbon is light gray, nitrogen is light blue,
oxygen is red. Notice again that the menu command affects only the
currently selected atoms.
Click on any alpha carbon of the protein and watch the command line. This is called "picking" an atom. When you click on an atom in the Main Window, RasMol identifies it. You should see something like this:
Atom: CA 652 Group: PRO 81
This tells you that you clicked on the alpha carbon (CA) of residue 81 in cytochrome b5, which is a proline. RasMol calls a residue a "group", and a nonprotein portion of the molecule, including a water molecule, a "hetero". If you clicked on some other atom, use picking to find this one.
If you can see a yellow atom in the ball & stick model, click on it. You should see
Atom: FE 754 Hetero: HEM 201
The yellow atom FE is iron (Fe3+, actually) in the center of the heme group of cytochrome b5. By using the command select hetero and not hoh, and then rendering in a contrasting style (as you did with Display:Ball&Stick above) you can quickly find nonprotein groups in the PDB file. By picking any atom in the group, you can learn the PDB name of the group, and thus know how to specify it in commands.
Note: Picking works best with Wireframe and Sticks displays, does not work at all with Ribbons, Strands, or Cartoons, and is somewhat unpredictable with Spacefill and Ball&Stick. This is not a great inconvenience, because Wireframe is the most useful display for exploring unfamiliar models in detail.
Listed below is the sequence of commands you have used so far. You can use this sequence to give you a quick overview of any macromolecule for which you have a PDB file, and to reveal any hetero groups (cofactors, inhibitors, water, and so forth) that are present in the file. The sequence is
Display: Backbone
Colours: Structure
Rasmol > select hetero and not hoh < return >
Display: Ball & Stick
Colours: CPK
Next you will learn how to manipulate the model. You can rotate it, move (translate) it to a different part of the screen, and zoom in or out.