On Mon, Jan 25, 2010 at 1:32 AM, Otis Rothenberger <o...@chemagic.com>wrote:
> Bob-
>
> 1. New question: We use Accelrys and Spartan to generate data.
> Accerrys calculates partial charge in nC and Spartan calculates this
> charge as esu. I never noticed this before. I assume that as long as
> partial charge sums to zero, Jmol will produce that same MEP,
> providing off course that the data is good and the calculations are
> comparable. Is this a correct assumption?
>
>
I was not aware of the difference in partial charge units. That will make
comparisons tricky.
> 2. While the Jmol right click menu MEP code is now looking much better
> to me, I don't understand why the following two JavaScript snips
> produce drastically different results. This JS is fed to my
> evalRasmol() function. The data in the second example is ethane from
> Accelrys:
>
> A)
> isosurface COLORSCHEME '" + colors + "'; isosurface resolution 6
> MOLECULAR color range all map mep;isosurface translucent;delay 2;echo;
>
> B)
> isosurface COLORSCHEME '" + colors + "'; isosurface resolution 6
> MOLECULAR color range -0.068 +0.023 map mep;isosurface
> translucent;delay 2;echo;
>
>
> If -0.068 and +0.023 are the Accelrys min and max, shouldn't the two
> code snips produce similar MEPs? As a point of information both
> Accelrys data and Spartan data for ethane produce:
>
>
yes, I think so. Check the charges on the atoms using
label %c
or
print {*}.partialcharge.min
print {*}.partialcharge.max
That should match what the isosurface command reports:
color range -0.14504099 0.041947186; mapped data range -0.14504099 to
0.041947186
with "all" these two should be the same.
> A) ROYGB all light up and ethane does, indeed, look like a
> nucleophile. Actually, this is what I expected "all" to do.
>
> B) More like the Jmol default. I expected that this would be the same
> as A - i.e. min to max = "all"
>
>
works for me -- both are the same -- . you might try not having the + there.
> Again, a point of information: Snip B) with -0.05 +0.05 essentially
> produces the Jmol menu MEP for both Spartan data and Accelrys data.
>
> that's what I would expect
> Otis
>
>
>
>
>
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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