When I initially implemented the transparent VdW engine for Avogadro I had the problem that any rendering of transparent objects must be done after the internal opaque objects have been rendered. So at the time I just implemented a ball and stick engine inside the VdW engine that was basically a copy of the ball and stick engine. I also mentioned that if we could set render order that would allow me to use any other engine if there was a way to ensure this engine was called after the others. The need for this had already been mentioned with respect to label rendering too.
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