no automatic way, but it would be a simple enough Jmol script.
Var atoms = {*}
Var n = atoms.length
Var minDistance = 3.0 # perhaps
for (Var i = 1; i <= n; i++) {
Var a = atoms[i]
for (Var j = i + 1; j <= n; j++) {
Var b = atoms[j]
if (b.distance(a) < minDistance) {
for (Var k = j + 1; k <= n; k++) {
Var c = atoms[k]
if (c.distance(a) < minDistance && c.distance(b) < minDistance) {
draw ID @{"d" + i + j + k} @a @b @c
}
}
}
}
}
On Mon, May 24, 2010 at 9:28 AM, Romuald Poteau
<romuald.pot...@laposte.net>wrote:
> Dear jmol users,
> I am working on clusters, which exhibit polyhedra structures not always
> easy to represent with balls and sticks.
> David Wales, at the origin of several papers on the topic of nanclusters,
> has adopted the representation that can be seen for example at :
> http://physchem.ox.ac.uk/~doye/jon/structures/Gupta/Cd/pictures.gif<http://physchem.ox.ac.uk/%7Edoye/jon/structures/Gupta/Cd/pictures.gif>
> Is it possible to do the same with jmol (I mean automatically) ? The
> polyhedra feature does not allow such drawing, which involves to draw
> triangular planes defined by all surface atoms and not polyhedra around a
> central atom (it may work in most cases by playing with the number of
> vertices, but it fails in the case of defects).
> Thank you for your help
> Romuald
>
>
>
> ------------------------------------------------------------------------------
>
>
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> Jmol-users@lists.sourceforge.net
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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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