Bob,
I'm in a heated discussion with my partner in this project right now re
what should be painted in a mep! Spartan evidently has lot's of ways to
tweak data presentations, and some of them seem flat out wrong.
Anyway, this leads to another question. The best of two worlds that
Spartan seems to be juggling (coloration of atom charge vs coloration of
surface charge resulting from atom charge, both of which Spartan seems
to execute at the surface!!!!!) would be a superimposition of
translucent Jmol surface coloring (mep) and partialCharge atom coloring.
This superimposition looks neat, and it tells the full story. Currently,
this partial charge coloring is set at rwb. Can this color range be
tweaked in Jmol Script? I think the rwb is great, but the intesity
variation is hard to see through the translucent mep.
Otis
Otis Rothenberger
chemagic.com
On 9/6/2010 12:41 PM, Robert Hanson wrote:
OK, I see. Right. Ranges were being set by actual atom charges, not
the ones out on the isosurface itself. This should be fixed. Will
upload and release.
On Mon, Sep 6, 2010 at 10:46 AM, Robert Hanson <hans...@stolaf.edu
<mailto:hans...@stolaf.edu>> wrote:
It's a bug in the color encoder for both 12.0 and 12.1. I'll take
a look at it.
On Mon, Sep 6, 2010 at 9:35 AM, Otis Rothenberger
<osrot...@chemagic.com <mailto:osrot...@chemagic.com>> wrote:
Bob,
The load filter picking up the ESP charges rather than the
Mulliken
charges works quite well.
Jmol 12.1.10_dev, however, seems to bring with it a change in mep
display. We're loading the cyclohexadienyl cation, and in
12.1.7, I
could light it up red through blue (explained below) with:
isosurface color range all resolution 6 solvent map mep
translucent
With the above script does not paint red through blue any longer.
I actually like what the above code produces (blue through
yellow), and
understandably it took the ESP charges to make this point. It's a
cation, and the above surface rendering code makes the EAS
direction
point we want to make, while at the same time declaring that
it's a dang
cation. BUT my partner in this project wants the surface
painting to
look "just like Spartan!" - all colors (roygb) over max min of
the cation.
The above Jmol code accomplished this in 12.1.7 - not so in
12.1.10_dev.
I've also tried the following in 12.1.10_dev with no success:
var x={*}.partialCharge.min;var
y={*}.partialCharge.max;isosurface color
range @x @y colorscheme "roygb" resolution 6 solvent map mep
translucent
var x={*}.partialCharge.min;var
y={*}.partialCharge.max;isosurface color
range all colorscheme "roygb" resolution 6 solvent map mep
translucent
var x={*}.partialCharge.min;var
y={*}.partialCharge.max;isosurface color
range @x @y colorscheme "roygb" resolution 6 solvent map mep
translucent
It gives the same chemically reasonable rendering - i.e. not
"just like
Spartan." Is there any way to still get the full color range
affect in
12.1.10_dev?
Otis
--
Otis Rothenberger
chemagic.com <http://chemagic.com>
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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
--
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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