Making objects semi-transparent is a potentially powerful means of viewing multiple layers of the molecule simultaneously. Imagine a protein on the surface of, and extending part way into, a membrane. One way to visualize the extent of the penetration is to represent the lipids as `Bonds' and make them transparent. That will show the membrane without completely obstructing the view of the protein.
If transparent views of a molecule seem to be obscuring other views, make sure all the transparent views in the Graphics form are farther down the list of views than non-transparent views.
Also, due to fundamental difficulties in GL/OpenGL, VMD will sometimes have problems displaying transparent objects when they are not drawn in a front-to-back order. If you click on the Transparent button on the Graphics form and rotate the molecule around you will see instances of this problem. VMD provides a script command to correct for this, but it tends to slow down the display update considerably. The command to type into the console window is ``display depthsort on'' . This will force VMD to arrange the objects in a front-to-back order by means of a depth sort. When many objects are on the screen, this sort can result in a substantial amount of calculation. Thus, it is best to first rotate the view around until you find an angle and style that you are happy with, and then turn depth-sorting on to enable correct transparency. The command to turn depth sorting off is simply ``display depthsort off.''
The transparent colors change their definitions automatically when the corresponding solid colors are redefined through the the Color form. Using text interface, however, requires changing the settings for the transparent colors explicitly.