On Mon, Jul 27, 2009 at 1:35 PM, Ralf Stephan <ralf@ark.in-berlin.de> wrote:
> I've looked into the generated molecules (something
> which I should I've done earlier) and the models now
> contain additional spheres as caps for the wireframe
> part of the default look.

... which leads me to another optimization: each bond
has two sphere caps, the center being the center of
both cylinder end circles. As far as I can see, the cylinders
are exactly overlapped such that the end cap spheres
are on the same position. So, two identical objects at the
same place. Removing one would give a further 20 per
cent reduction in size.

Compared to other objects, the sphere's don't amount to much. Yes, 20% is significant, but surfaces are the real issue. In any case, it's probably not worth it to go to all the trouble to figure out that a bond already has an endcap there.
 
If you remove only those with identical
parameters, you still can remove the CPK part and have
a perfectly smooth wireframe. Of course you could have
much more if you make the molecule out of those pieces
(sphere+half bond) that have the same material, anyway,
but you then lose being able to separate CPK and wire.
I personally could care less, however. If I want wire only,
I turn off CPK in Jmol and export then, that's it.

Is there a chance to see one or the other optimization?

Best,

ralf



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Robert M. Hanson
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