Otello,
It will be fine. Just make sure you have loaded all 9 unit cells around the
area you wish to see. That way you will have it. If the data is n{ot a CIF
file or does not have unit cell data, that's no problem. Basically what you
do is define the unit cell and symmetry (if desired) on the LOAD line after
the file name, and Jmol will load the file as though it had that unit cell
and symmetry. This is one of the very coolest features of Jmol and should be
perfect for this if you need it.
load "myfile" {3 3 1} unitcell {6.00 6.00 6.00 90 90 120}
or maybe
load "myfile" {445 665 1} unitcell {6.00 6.00 6.00 90 90 120}
(which centers the unit cell in the set of 9)
Ah, except perhaps that is not set up for slab yet....
Oh, I know. Just make that c parameter very large. Jmol will keep your
coordinates in Cartesian format despite what you put in for the unit cell.
Then, if you need to, you can move the unit cell into the structure using,
for example:
unitcell {6.0 6.0 0}
or
unitcell {2 2 1/}
You may have to experiment, and if it doesn't work for you, let me know.
I think you will find everything there for what you need. Jmol has extensive
capability in exactly this area.
Be sure to use
isosurface LATTICE
because that will save you hugely on memory.
Bob
On Sat, Jul 31, 2010 at 6:13 AM, Otello Maria Roscioni <
rosci...@fci.unibo.it> wrote:
> Dear Bob,
>
> thank you for the useful suggestions. Using the command:
>
> isosurface ID "iso1" slab within [{0 0 -1000}, {0 0 2000}, {0 57.108 0},
> {57.108 0 0}] sasurface lattice {2 2 1}
>
> the isosurface looks much more correct. However, it is not computed
> properly at the bounday of the unit cell, as you can see here:
>
> http://img696.imageshack.us/img696/9476/f1288.png
>
> I suppose the problem is that the probe used to compute the isosurface
> does not consider periodic images for atoms at the unit cell boundaries.
> Anyway, I can show just the unit cell and pretend that the corresponding
> isosurface is correct ;)
>
no error there -- I think you just didn't have a full set of 9 unit cells.
>
> By the way, there is a small bug in the SLAB PLANE (or more likely in
> WRITE IDTF) command: when exporting the scene in IDTF format, the
> resulting object contains the whole system and not the sliced plane.
>
>
Ah, that's interesting. Thanks.
--
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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