A much better sphere can be made now using the ellipsoid command.
ellipsoid e1 center {0 0 0} axes {1 0 0} {0 1 0} {0 0 1} scale 2.0
http://chemapps.stolaf.edu/jmol/docs/?ver=11.6#ellipsoid
Bob
Angel Herraez wrote:
>>1) Is it possible to draw a sphere, filled or sketched like the one
>>on: http://accelrys.com/products/discovery-studio/pharmacophores/
>>pharmacophore.jpg or http://www.biomedcentral.com/content/figures/
>>1471-2210-6-11-7.jpg?
>>
>>
>
>Yes, you can draw spheres using "isosurface" and make them
>opaque/translucent; not sure about mesh-wire, but maybe
>
>A bit outdated doc, but simpler and still useful:
>http://biomodel.uah.es/Jmol/surfaces/inicio.htm#nonMol
>and the full doc:
>http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#isosurface
>
>
>Example (sphere around atom):
>
>isoSurface mySphere center (atomno=6) sphere 1.5 mesh nofill
>
>or around the center of an atom set:
>
>isoSurface mySphere center (C2, C3, C4) sphere 1.5 mesh nofill
>
>or in a 3D coordinate:
>
>soSurface mySphere center {1.5 0 -0.5} sphere 1.5 mesh nofill
>
>(play with mesh/nomesh, fill/nofill, dots/nodots, opaque/translucent)
>
>
>
>>2) Can I add atoms/bonds via the scripting language? If not, I guess
>>I can create a simple input file and append it?
>>
>>
>
>Probably both ways.
>
>Bonds are created using "connect":
>
>connect (C1) (O3)
>connect (C1) (O3) double
>
>Atoms... maybe with the "data" command, but I'm not used to that. You
>can also fake them as big dots using "draw", depending on your needs
>ยท
> Dr. Angel Herraez
> Dep. Bioquimica y Biologia Molecular, Universidad de Alcala
> E-28871 Alcala de Henares (Madrid), Spain
>
>
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--
Robert M. Hanson
Professor of Chemistry
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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