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I realize that transparent images can be confusing. However, it is particularly nice in this case, because it allows the user to get a sense of the relative orientation of the isosurface to the underlying molecule which it surrounds.
Bill mentioned sorting the transparent polygons as a possible solution. If the (isosurface) polygon data structure is accessible from VisAD, would implementing a simple z-sort of this list be possible? I am not so concerned of a 'real-time' z-sort as the user rotates the molecule; a simple z-sort at the end of rotation would be sufficient to ensure that they have a nice looking picture after they get things into the desired orientation. Would this be a reasonable approach, or a futile waste of time?
If this works out, I would be happy to contribute the resulting code.JR Schmidt
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