Hi Bob,
Thanks for your help. I think I understand now how it works. It is
indeed tricky, but I think I can get it to work.
However, I still have a few problems:
I cannot use the cell selection, as this is too crude. I need to
specify fractions of cells, i.e. I may need boundaries such as {-0.2
1.2 -0.3 1.3 0 1.0} in order to get nice tubes. So I have
written a small program that gives me two models, one with all atoms
within the desired range and one with only atoms outside this
boundary. By selecting only the "inside" atoms of the first model I
get the desired open tubes. This works, but maybe there is a cleverer
way to do this. The openings are a bit jagged, but I think this
cannot be changed.
So far so good. Now the problem: in order to get the channel system,
we fill it with spheres that have different radii. I want now to
calculate the surface around these "atoms", so I need to specify
their radii in Jmol. I tried it with spacefill, which works fine for
the atom display, but these are not used in the calculation of the
isosurface. I need to define the VDW radii myself, but I did not find
a way to do this. Is there one?
Of course, I will be glad to send you the result of my efforts. So
far I have only an experimental page which is not yet properly
connected to the zeolite database and which shows no channel surface
yet. :-)
look at
http://crystals.ethz.ch/IZA-SC/3D-images/JmolViewer.php?
cifname=LTA&FTC=LTA&acell=%2011.919&bcell=%2011.919&ccell=%
2011.919&alpha=%2090.000&beta=%2090.000&gamma=%2090.000
to see just one example of a zeolite (all on one line)
Cheers
Christian
> Date: Tue, 10 Apr 2007 10:28:40 -0500
> From: "Bob Hanson" <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] slab/depth in more than one direction
> To: [EMAIL PROTECTED]
> Message-ID:
> <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hmm, this is tricky, and the solution may not be practical.
>
> 1) The internal arbitrary-plane slabbing is specifically for atoms,
> not surfaces. So you can select atoms this way, but you cannot cut
> surfaces with it.
>
> 2) All you need is a few more atoms. Instead of building a single
> unitcell, make 27 using
>
> load xxx.cif {444 666 1}
>
> Now you only DISPLAY the center cell:
>
> display cell=555
>
> but all the other atoms are there, so when you do
>
> select displayed
> isosurface sasurface
>
> you will get the isosurface for the atoms you see, and you will get
> those open ends you are talking about. (Please show me -- I love
> zeolite structures.)
>
> Also, I would recommend trying
>
> isosurface sasurface 0
>
> not just "sasurface". The default there is whatever is set as the
> current solventProbeRadius, which has a default of 1.2 Angstroms. I
> would think (maybe) what you want for your display is 0, which gives
> the van der Waals radius surface instead. Maybe?
>
> Also, have you checed out
>
> isosurface hkl {h k l} map sasurface
>
> ? This is a very cool-looking plot.
>
>
> Bob Hanson
>
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