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Hi,
Here are three different views of the triazene (N3H3) molecule.
Top left: electron density
Top right: electrostatic potential
Bottom left: Laplacian of the electron density
All the three "clouds" are rendered from .df3 files generated with the help
of quantum calculation software (gaussian98, if you care). I have been
playing with isosurfaces as well, but it's not easy to get the scale from
the .df3 files (all values are between 0 and 1) and there are some issues
with the onion-like layers in the Laplacian.
--
light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby
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Attachments:
Download 'triazene.jpg' (28 KB)
Preview of image 'triazene.jpg'
![triazene.jpg](/povray.binaries.images/attachment/%3C417bf122%40news.povray.org%3E/triazene.jpg?ttop=441697&toff=6000&preview=1)
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Very interesting, good work!!!
Regards,
Oleguer
news:417bf122@news.povray.org...
> Hi,
>
> Here are three different views of the triazene (N3H3) molecule.
>
> Top left: electron density
> Top right: electrostatic potential
> Bottom left: Laplacian of the electron density
>
> All the three "clouds" are rendered from .df3 files generated with the
help
> of quantum calculation software (gaussian98, if you care). I have been
> playing with isosurfaces as well, but it's not easy to get the scale from
> the .df3 files (all values are between 0 and 1) and there are some issues
> with the onion-like layers in the Laplacian.
>
> --
> light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
> 9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
> 0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby
>
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"Jellby" <jel### [at] M-yahoo com> wrote in message
news:417bf122@news.povray.org...
> Hi,
>
> Here are three different views of the triazene (N3H3) molecule.
>
> Top left: electron density
> Top right: electrostatic potential
> Bottom left: Laplacian of the electron density
>
> All the three "clouds" are rendered from .df3 files generated with the
help
> of quantum calculation software (gaussian98, if you care). I have been
[snip]
Are you using the linux version of gaussian98?
http://www.gausian.com is not responding.
http://www.compuchem.com/gaussian.htm
is about gaussian 03 W for windows, but the download link is
void of any further mention of the software
Any clues on where/how to obtain some version of gaussian?
And,
is it stratightforward to produce the .df3?
tia,
Pan
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Among other things, pan saw fit to write:
> Are you using the linux version of gaussian98?
> http://www.gausian.com is not responding.
>
> http://www.compuchem.com/gaussian.htm
> is about gaussian 03 W for windows, but the download link is
> void of any further mention of the software
>
> Any clues on where/how to obtain some version of gaussian?
Yes, we have the linux/unix version of gaussian98 in my department. I can't
tell you exactly the address you should write to, but gaussian.com was
working yesterday, so I guess it's a temporary a temporary problem. Anyway,
gaussian is not free, you may want to try other programs as GAMESS (I'm not
sure whether it can output electron density data, but it's very likely)
> And,
> is it stratightforward to produce the .df3?
It's easier than it could seem. It's easy to get the density (or potential,
or laplacian...) in a grid, then all you need is convert the ascii,
floating-point values to the correct .df3 format.
--
light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby
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Hi Jellby,
just a question. What do You think, is it somehow possible to create a 3
dimesional electron density map from a single crystal x-ray measurement,
using povray for the visualisation. Or would it be somehow possible to
calculate a 3df file from a hkl file using fourier synthesis. It's possible
to calculate 2 dimensional electron maps from the data during the structure
refinement. But a 3 dimensional one ???
Nice work by the way.
Shu.
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Jellby wrote:
> Hi,
>
> Here are three different views of the triazene (N3H3) molecule.
>
> Top left: electron density
> Top right: electrostatic potential
> Bottom left: Laplacian of the electron density
>
> All the three "clouds" are rendered from .df3 files generated with the help
> of quantum calculation software (gaussian98, if you care). I have been
> playing with isosurfaces as well, but it's not easy to get the scale from
> the .df3 files (all values are between 0 and 1) and there are some issues
> with the onion-like layers in the Laplacian.
>
>
>
> ------------------------------------------------------------------------
>
Very nice. Are you familiar with the Orbitron?
http://www.shef.ac.uk/chemistry/orbitron/
--
Maurice
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Among other things, Shurakai wrote:
> just a question. What do You think, is it somehow possible to create a 3
> dimesional electron density map from a single crystal x-ray measurement,
> using povray for the visualisation. Or would it be somehow possible to
> calculate a 3df file from a hkl file using fourier synthesis. It's
> possible to calculate 2 dimensional electron maps from the data during the
> structure refinement. But a 3 dimensional one ???
No idea, sorry. I have never worked with x-ray experiments, but I guess it
should theoretically be possible to get the 3D density. If you can obtain
the density values in a 2D grid, maybe you can combine several planes to
get a 3D grid...
The images I've shown are from theoretical calculations, and the software
already outputs a 3D-grid of density data, all that's needed is a format
conversion.
--
light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby
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Among other things, Maurice saw fit to write:
> Very nice. Are you familiar with the Orbitron?
> http://www.shef.ac.uk/chemistry/orbitron/
Yes, I've visited it several times, it's very nice. Note, however, that the
information displayed there and in my images is different.
--
light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby
Post a reply to this message
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Jellby wrote:
> Among other things, Maurice saw fit to write:
>
>
>>Very nice. Are you familiar with the Orbitron?
>>http://www.shef.ac.uk/chemistry/orbitron/
>
>
> Yes, I've visited it several times, it's very nice. Note, however, that the
> information displayed there and in my images is different.
>
Yes, I know.
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