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Transparency

 

Making objects semi-transparent is a potentially powerful means of viewing multiple layers of the molecule simultaneously. VMD sometimes has some problem drawing transparent objects when they are not drawn in the proper front-to-back order. Unfortunately the only way to determine when it will work properly is through trial and error. With this disclaimer, there are some times when drawing transparent objects is useful. 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.



Andrew Dalke
Tue May 14 16:49:45 CDT 1996