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
On 4/10/07, Christian Baerlocher <[EMAIL PROTECTED]> wrote:
> Hi All,
>
> I am fairly new to Jmol, but I found it very useful to calculate the
> channel system in zeolites using the command isosurfaces. These
> channels systems consist of interconnected "tubes" and the
> connections are in general three dimensional.
>
> I have only two problems and I wonder if there is an easy solution to
> them.
>
> I use the command "isosurface sasurface" to calclulate these
> "tubes". This works fine except that the tubes are closed at the
> end, which of course they should not be as they are continuous
> through the crystal. I can open them up by using the commands "slab"
> and "depth" (with slab set), but so far I have found that I can do
> that only in two opposing direction at a time.
>
> So my first question is: how can I use "internal" slab/depth in more
> than one direction at the same time? I would be happy if I could
> clip the channel system parallel to all of the 6 faces of the unit
> cell (i.e. using slab/depth x% along the 3 axes))
>
> I would like to include these channel system on our zeolite web page.
> It would be great, if I could save the "clipped" isosurfaces in jvxl
> files. How can I do this? I fact, if I knew how to do this, I could
> read a slab file in again, apply a new slab/depth in an other
> direction and save it again. This could be a solution to my first
> question, if there is no other way.
>
> Thanks for you help.
>
> Christian
>
>
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