Let's start from scratch by deleting everything: use the text console and tye the command mol delete all and press enter. This deletes all loaded molecules and is often more convenient then selecting them and deleting them all one by one. Alternatively, you could highlight each molecule in the molecule browser, and use the Delete Molecule item in the Molecule menu to remove them one by one.
Begin by loading the mbco.pdb structure with the Files window. Turn on just the heme, CO, and histidines by using the selection commands resname HEM CO or resid 64 93. The dot (probably green) in the middle is the iron and you can verify that by picking it with the mouse. Do this by changing the ``Object Mode'' pull-down to ``Pick'', and selecting ``Atoms'' for the pick mode in the Mouse menu. The label HEM154:FE should appear both on the display and in the text console.
Change the pick mode in the Mouse menu to ``Bonds''. To get the distance between the iron and the oxygen of the CO, click with the left mouse button first on the iron and then on the oxygen. The first click turned the FE label on and the second turned the O label on and drew a line between the two atoms with the distance drawn in the middle and a bit to the right. The distance between the two atoms is 2.94 Å, as compared to 2.93 Å in the paper; not bad. However, picking the distance between the FE and the C of the CO reveals a distance of 1.91 Å as compared to 1.85 Å in the paper. The difference is that the structures in the VMD distribution are actually preliminary structures obtained before the final coordinates were determined.
In order to experiment with more complex picking modes, consider the angle made by the O of the CO with the FE of the heme and the NE2 of residue 93 (you can click on the atoms to find which ones are which). Using the Mouse menu, change the pick mode to ``Angles''. This should cause the cursor to become a red crosshair. Click on each of the three atoms using the left mouse button. After the third pick, a shallow angle will appear indicating an 8.71 degree angle between the three atoms.
Now load the intermediate star.pdb file which can also be found in the proteins directory of your distribution. Again use the Files window to do this. Both of the molecules will be loaded side by side. Go to the Graphics window and change the selection so it the same as the first, i.e. resname HEM CO or resid 64 93. The two molecules are almost atop each other, making it hard to distinguish the two, so change the colors to simplify things.
First, in the Graphics window, change the Coloring method to `Molecule'. Use the Selected Molecule chooser to change the mbco.pdb Coloring method to `Molecule' as well. Open the Color window and scroll the Category browser down until the line `Molecule' is visible. Click on it then click on the line which says mbco.pdb. (There may be two mbco lines if the file had been loaded before in this session.) Scroll the Colors browser up to click on `blue'. This should change one of the molecules in the display to blue.
Next, click on the last line in the Names chooser, which says star.pdb. This time, choose `red' from the Colors chooser. The display should be much easier to understand. The myoglobin with the bound CO is in blue and the intermediate state is in red. At this point it is easy to measure the change in position between the two different states by using the middle mouse button to pick the same atom in the two conformations.
Once that is done, it is easy to point out one interesting aspect of the way VMD handles the graphics. Go to the main window, select one of the two molecules, and press Toggle Fixed. Enter translation mode and move the other molecule around. Notice that the number which lists the distance between the two atoms never changes. That's because the mouse only affects the way the coordinates are translated to the screen image. It does not affect the real coordinates at all. It is possible to change the coordinates in a molecule using the text command interface, or by using the atom move pick modes).
By the way, unfix the molecules and do a `Reset View' from the Display menu to reset everything. Load up the third structure, deoxy.pdb and give it the same selection as the other two molecules. However, color this one green. Pull out Nature v. 371, Oct. 27, 1994 and turn to page 740. With a bit of manipulation you should be able to recreate the image that appears there.