Great, thanks!
Can I make the lines in the 'mesh' thicker in some way? They are hard
to see on white background if a large molecule. Looked in the
scripting doc for isosurface but did not see any option for that.
What I did see was that with resolution 2 or three, for example:
"isoSurface mySphere color green resolution 2 center {-3.3021 3.1716
0.3118} sphere 1 mesh nofill"
the sphere is trunkated. Is this deliberate on too low resolutions?
Cheers,
/Ola
On Jul 2, 2008, at 11:09 , 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A bit outdated doc, but simpler and still useful: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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