Paul and Robert,

Thank you very much for your responses.
They are very helpful.
I do have a couple of more questions – I hope that you do not mind.
Am I wrong about the reflection looking different for the oxygen versus the carbon?
If I export a jpeg they look fine, only when I try to export a povray do they look different.
Is there an easy way to fix this?  I do not want to manually change the povray files – I guess
that I could write a script to edit them.

Thank you again.
Jay




From: Robert Hanson <hansonr@stolaf.edu>
Subject: Re: [Jmol-users] jmol, povray export of oxygen
To: jmol-users@lists.sourceforge.net
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        <AANLkTimmLIgY9NVjXuJ1V9N-E1fwUh7701s2LJnVW1b6@mail.gmail.com>
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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 <
paul.pillot@ac-orleans-tours.fr> 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}
> #end
> #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}
>  #end
> #end
> 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...
>
> -Paul
>
> Le 28 juin 2010 ? 21:20, Shore, Jay a ?crit :
>
>
> Howdy,
>
> 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
>
> --
> Jay Shore
> Department of Chemistry and Biochemistry
> South Dakota State University
> Brookings, SD 57007
>
>
>
>
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>


--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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