You have already seen that VMD can label individual atoms by simply clicking on them with the mouse. In addition, VMD supports several other picking modes. For a listing of them, hold down the rightmost mouse button in the GL Display to reveal the popup menu. Drag down to the Pick Item Mode submenu. By default, VMD is in the "Query" mode, allowing you to pick atoms and display labels. If you switch to "Center" mode and choose an atom in the display, then subsequent rotations will be performed about this atom position. In essence you will have picked a new center of rotation. Another useful picking mode is "Bonds." If you select this option and click on two atoms in the display window, a dashed line will be drawn between them and the distance separating them will be calculated. To familiarize yourself with this option, try clicking on two atoms of the bR retinal residue. Choose one atom from the segment which remains in the binding pocket, and the second atom from the cleaved portion which is pulled outward. If you then animate the system, you will see how the distance between the two retinal pieces increases over the course of the simulation. If you would like a graph of this distance over time, try this: hold the rightmost mouse button down in the GL Display window. Drag down to "Show Form" in the popup menu and choose "labels". In the upper left corner of labels, change the Category to Bonds. Click on one of the entries which appears in the blue browser window and hit the "Graph" button. A plot of the bond length over the course of the simulation will appear.
Similar in spirit to the "Bonds" picking mode are "Angles" and "Dihedrals." In these modes, you should click on three or four atoms respectively to calculate the angles defined by those collections of objects.
Finally there are the Move options. If you choose MoveAtom and select an atom in the display window, you will be allowed to drag it about the screen to change its position. For instance, suppose you wanted to refine a bond length by hand in VMD. One would first choose the "Bonds" picking mode and calculate the distance between the two atoms forming the bond. Then you would select "MoveAtom" and drag one of the atoms to the desired bond length. The distance will be updated and displayed on the screen automatically. A similar strategy could be used to modify bond or dihedral angles by hand.
When one does a lot of picking in VMD, the display tends to get cluttered. You can selectively delete output from picking actions by using the popup menu's "Labels" option.