RMSD Calculations
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.