Now that you have learned a bit more about picking, lets try to apply this knowledge in our study of bR. Recall that the goal of the simulation was to determine if the retinal could be pulled through the hole without destroying the structural character of the rest of the protein. One way to test whether or not this was accomplished is through an RMSD calculation. This will quantify the difference between the first and last structures of the animation.
Until now we have worked exclusively with just one molecule in VMD. However, if we are to compare the first and last frames of the simulation, we must have a way to simultaneously load two structures. It turns out that this is very easy to do in VMD, as will be demonstrated with an example. First go to the animate menu and click on the button marked "End." This will allow you to specify the last frame of the simulation as one of the molecules forming the basis for the RMSD. Now we must simultaneously load the first frame of the simulation. Open the molecules form and load the "pdb only" file segbR.pdb again. It may be difficult to tell the two molecules apart on screen, so we also recommend that you go to the graphics menu and choose the Coloring Method "Molecule" as well. This will increase the contrast between the two coordinate sets. Now that the two molecules are loaded, the rest is a snap. Hold down on the rightmost mouse button in the GL Display to reveal the popup menu. Drag down to the Fit option and choose "Two Molecules: CA Atoms" in the submenus. You have now specified that an RMSD calculation involving all carbon alpha atoms of two molecules should be applied. However, you must still tell VMD which two molecules should be used. It is true that there only two molecules presently on the screen, but there could just as well be five or ten. VMD has no limit on the number of molecules which may be simultaneously displayed. For this reason you will have to explicity indicate which two molecules to compare. This can be done by "picking" one atom in each of the two molecules. Try experimenting with other fitting options to learn more about this VMD feature.