Thanks, Rick. I did realize that (finally) last night and was able to tap right
into it. THANK YOU, MIGUEL!!!
So look at http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm and see
if it fits the bill.
Notice that each slice is about 6K -- a bit of an improvement, I think. (And if
you REALLY want a fair comparison, gzip that!) So far the compression is pretty
close to 500:1 in just about all the cases, and you can put as many slices in
one file as you want. If you then use that file for the "load" command
I still have to figure out a good way to make these JVXL files easily produced.
I could do it with a website, but I'd like to make Jmol.jar be able to do that.
I'm uncertain about that method of defining planes -- is the {a b c d} notation
acceptable? Where:
ax + by + cz + d = 0
Or is there a different standard I should be using?
isoslice is an idea; I just stuck with the isosurface command, substituting a
plane definition for the first file, since that's really what it is -- a
specific sort of surface that is going to be mapped.
Bob
rspinney wrote:
rspinney wrote:
Hi Bob,
The mapped surfaces require a second cube file. The most common situation
is
where the electrostatic potential (ESP) is mapped onto the total electron
density surface. The electron density surface is constructed as you
described, and once the grid points defining the surface have been
determined they are used to determine the value of the ESP from the
second
cube. The ESP value then determines the color at that point of the
surface.
Ah, then we are all set. I have those two files for CH3Cl. That
explains their common point grid. Makes total sense. I do not believe
this has been considered in Jmol. I want to introduce that. All
suggestions for command syntax welcome. The word "map" would be
appropriate here.
This function already exists in Jmol (eg. See
http://undergrad-ed.chemistry.ohio-state.edu/Carey5th/Ch04/ch4-2-1.html )
where the commands
'isosurface plus 0.0004 "../mapped/ch3oh-density.cub.gz";' +
'isosurface plus color "../mapped/ch3oh-esp.cub.gz";' +
First command loads and generates the electron density surface, and the
second one maps the ESP onto the density surface. The only problem is the
size of these files, even the "small" ones are 200 Kb, and the larger ones
up to 2 Mb (when gzipped). This of course produces slow download times
especially over dial up.
A slice through a cube would have one value defined by the user (i.e. a
slice at X=0). The surface could then be color coded by the value of the
grid point from the cube file.
Yes, this sounds quite reasonable. So you get a colored plane. Please
suggest a command syntax.
How about isoslice ? i.e.
isoslice [name] [color range] "cube-file-name"
Bob
--
Rick
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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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