[note: this message relates to the experimetal prototype "Jmol 10.x" not
the public release Jmol 10.2. See
http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm for details.]
The JVXL format is a GO.
color mapping works fine; storage of multiple surfaces in the same file works as
well. Compare some file sizes:
color maps
----------
CH3Cl density and electrostatic potential:
09/29/2005 08:18 AM 1,813,012 ch3cl-density.cub
09/29/2005 08:19 AM 1,813,021 ch3cl-esp.cub
Jmol 10.2:
load ch3cl-density.cub; isosurface "ch3cl-density.cub" color "ch3cl-esp.cub"
g-zipped:
05/24/2006 02:37 PM 600,830 ch3cl-density.cub.gz
05/24/2006 02:37 PM 592,942 ch3cl-esp.cub.gz
load ch3cl-density.cub.gz; isosurface "ch3cl-density.cub.gz" color
"ch3cl-esp.cub.gz"
and combined in one JVXL file:
05/24/2006 06:47 PM 6,206 ch3cl_map.jvxl
<http://www.stolaf.edu/people/hansonr/jmol/test/proto/ch3cl_map.jvxl>
Jmol 10.x:
load ch3cl_map.jvxl; isosurface ""
So mapping is no problem.
Orbitals
--------
five separate fairly low-resolution orbitals:
05/24/2006 08:28 PM 920,240 dx2y2.cube
05/24/2006 08:28 PM 920,240 dxy.cube
05/24/2006 08:28 PM 920,240 dxz.cube
05/24/2006 08:28 PM 920,240 dyz.cube
05/24/2006 08:28 PM 920,240 dz2.cube
Jmol 10.2:
load dxy.cube; select hydrogen; spacefill off;isosurface "dxy.cube"
load dyz.cube; select hydrogen; spacefill off;isosurface "dyz.cube"
load dxz.cube; select hydrogen; spacefill off;isosurface "dxz.cube"
load dx2y2.cube; select hydrogen; spacefill off;isosurface "dx2y2.cube"
(but this one, I think, is still xy)
load dz2.cube; select hydrogen; spacefill off;isosurface "dz2.cube"
and combined in a single JVXL file:
05/24/2006 08:32 PM 9,824 d_orbitals.jvxl
<http://www.stolaf.edu/people/hansonr/jmol/test/proto/d_orbitals.jvxl>
Jmol 10.x:
load d_orbitals.jvxl;select hydrogen; spacefill off
isosurface fileindex 1 ""
isosurface fileindex 2 ""
isosurface fileindex 3 ""
isosurface fileindex 5 ""
and two different cutoffs to show orbital phase (one +, one -):
ethene HOMO:
07/29/2005 12:13 PM 1,012,379 ethene-HOMO.cub
05/22/2006 05:50 PM 358,960 ethene-HOMO.cub.gz
05/24/2006 02:37 PM 5,526 ethene.jvxl
<http://www.stolaf.edu/people/hansonr/jmol/test/proto/ethene.jvxl>
Jmol 10.x:
load ethene.jvxl;isosurface p1 fileindex 1 ""; isosurface p2 fileindex 2 "";
Right now what I'm doing is clipping the files themselves from system.out.
But it's all set up to simply deliver the file code to, say, a textarea, if we
wanted it to.
next stop: colored planes.
Bob Hanson
--
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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