On 9/7/2012 1:03 PM, Robert Hanson wrote:
The polyhedron needs a central atom. But you can add that yourself.
The command appears to be undocumented --
assign {attachmentAtom} "Symbol" {x y z}
For example:
assign atom {atomno=14} "Cl" {2 3 4}
That position {2 3 4} could also be an average position of a number of
atoms:
assign atom {atomno=14} "Cl" {2 3 4} {atomno=14 or atomno=13 or
atomno=12 or atomno=11}
then you would also need to do the connections before creating the
polyhedra.
HOWEVER, with a bit of a tweak of Jmol, I can make this possible
without connecting the atoms. You will still need a central atom,
though. Let me get back to you on this.
Bob
Could the tweak include the option of drawing polyhedra if not all
"vertices" are present? Such as a tetrahedron for ammonia or water?
Something that would draw a polyhedron when the central atom and a
number of vertices is specified with the size equal the specified bond
(something like O1 4 O1-H 1 for water)..
I know I am asking too much, but if you are tweaking it...
Thanks
PM
On Fri, Sep 7, 2012 at 8:16 AM, Nikolay Bogdanov
<nikol.bogda...@gmail.com <mailto:nikol.bogda...@gmail.com>> wrote:
I'm trying to make a figure showing the coordination of metal ions
in crystal - they form network of tetrahedra. I can do this with
bonds, but the
figure looks confusing. It would be much more clear with opaque
tetrahedrons.
As I understand Jmol builds polyhedra around some central atoms,
which are missing in my case. So I wonder is there a way to build
the polyhedra just
from bonds.
Thanks,
Nikolay
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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