Otello,
You can do that.
Jmol 12.0 includes the option LATTICE {i j k} for the isosurface command.
You might want to take a look at that. In combination with isosurface SLAB
UNITCELL, this works great. You basically just create the isosurface for one
unit cell with SLAB -- and then use the LATTICE option to multiply it as
many times as you want.
Ah, now I did just fix a bug I see there. I never implemented that option
for slab- and polymer-based unit cells. I think there's only one file reader
-- Crystal (i.e. Crystal09) -- that can generate models with slab or polymer
symmetry. So unless that's what you are using, it doesn't matter anyway.
But you can "fake" that if you want. What you would do is create a SLAB
based on an elongated unit cell:
isosurface ID "isosurface1" slab within [{0 0 -1000}, {0 0 2000.0}, {0.0
2.9769197 0.0}, {2.9769197 0.0 0.0}] vanderWaals;
That WITHIN array is [center c b a]. I don't know how I got that c b a
instead of a b c, but I did. That may not even be documented, but it's what
Jmol creates for it's state when you use "isosurface SLAB UNITCELL...". My
point is just that you can put whatever numbers in there you want. By moving
the center down in Z and making c twice that distance, we get that slabbing
effect you are talking about -- slabbing along the crystallographic a and b
axes and no slabbing along c.
Bob
On Thu, Jul 29, 2010 at 10:29 AM, Otello Maria Roscioni <
[email protected]> wrote:
> Dear Jmol users,
>
> is there a way to display isosurfaces (say, solvent accessible surface) of
> slabs considering periodic boundary conditions? It should be done by
> computing the isosurface for the top and bottom faces of the slab,
> ignoring the sides.
>
> Hope I made my request clear!
>
> Thank you very much for any advice I will receive.
> Otello.
>
>
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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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