The first three a() entries are the atoms. The other 8 are end-caps for the bonds. Hidden in this case by the atoms and the opacity of the bonds themselves. 

On Mon, Jun 28, 2010 at 2:58 PM, Paul Pillot <> wrote:
Recently I have played a bit with some pov outputs in order to set more precisely the effects I wanted for each atom.
To do that, I changed the last settings in the corresponding spheres (translucent factor). Then I edited the macro for the translucent finish so that the corresponding translucent factor could lead to the desired reflection or transparency effect. 
Here is an example of the macro I used :
#macro translucentFinish(T)
 #local shineFactor = T;
 #if (T > 0)
  finish {
   ambient 0.3
   diffuse 0.84
   specular 0.32
   roughness .00001
   phong 0.8
   phong_size 40
   reflection 0.4
  interior {ior 1.33 caustics 0.1}
#if (T < 0.1)
  finish {
   ambient 0.45
   diffuse 0.84
   specular 0.32
   roughness .00001
   metallic 0.5
   phong 0.9
   phong_size 120
   reflection 0.25
interior {ior 1.5}
It's a trick, but that may help you setting a scene that would suit your needs...

Regarding the number of spheres and cylinders : there are indeed 8 different cylinders in your image : 2 doubles bonds, each having a grey and a red part (2x2x2=8). I can't find any explanation to the number of spheres...


Le 28 juin 2010 à 21:20, Shore, Jay a écrit :


I loaded carbon_dioxide.mol in to jmol and then exported the povray file and the reflectance on the oxygen looks different than the reflectance on the carbon.  I have also tried water and saw that the reflectance on the oxygen was different than that on the hydrogen.

Also, in the pov file, it seems like it is drawing the spheres and tubes multiple times.

Am I missing something?
Any help or suggestions would be appreciated.


Jay Shore
Department of Chemistry and Biochemistry
South Dakota State University
Brookings, SD 57007

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