Jellby wrote:
> Among other things, Shurakai wrote:
> 
> 
>>and a side-view of it.
> 
> 
> If I'm not mistaken, those ellipsoids are a representation of the confidence 
> region for the position of the nuclei. Could you replace them with simple 

Never. The confidence region for the nuclei is spheric. The confidence 
region for the electrons is much more complex. Have a look at the 
Orbitron for renders of most common electron-clouds:

http://www.shef.ac.uk/chemistry/orbitron/

> spheres (proportional to Van der Waals radii, for example)? Or maybe make 
> all spheres and cylinders (bonds) the same size?
>

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