"Q: After this change, did everything else seem to work for you?"

Yes, it does. As I said, I didn't find it broke anything. I opened lots of molecules with different color settings
and everything worked normally. I later figured from your Colix code that commenting out that line should be
harmless, because colors default to an alpha value of 255 unless otherwise specified. If no one can pass
in an alpha value through scripts, you should rest assured that colors always default to opaque.

Q: What is the 'background' for the images that you are creating?

We are using Jmol as a layer in a multi-layer container, in which there can be other Java2D objects behind
or in front of the Jmol layer. Thus, transparency is needed.

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