I went around to installing the plug-in. The default animation is pretty cool.
If you rotate a big molecule the movement is jerky, you need more frames in the
anumations. The pics displayed in 1:1 ratio on my monitor, but it looks like the
renders are set for a 4:3 monitor?
I suppose most of the users will know what atoms are where, but for laymen like
me you should include a legend indicating the atoms colour.
The highlight on the spheres is strange but not uncool.
I must say I was amazed at the number of molecules you have in there!

Oh, and some stuff isn't in English.

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