Otis -- all about surface types, below.
On Wed, Sep 15, 2010 at 12:24 PM, Otis Rothenberger
<osrot...@chemagic.com>wrote:
> Bob,
>
>
> On 9/15/2010 11:47 AM, Robert Hanson wrote:
>
> Charges at atoms have to be summed using q/r for each point on the
> isosurface. So the values at the surface are different from the values at
> the atoms (smaller values). For example:
>
>
> OK, I get it. The first data range in the message is the data range for the
> computed surface charge points. If I use "color range all," then the
> following message type is returned:
>
>
> data range 0.28645405 to 0.5315478 with color scheme spanning 0.28645405
> to 0.5315478
>
> The expression "color scheme spanning" takes on the value of the calculated
> surface data range. If however, in the Jmol script, I set a color range
> based on the actual atomic charges, then this "color scheme spanning"
> reports the value of my Jmol script charges. Is this just a message
> reporting peculiarity?
>
so you have two ranges -- the actual data (shown first) and the range you
have designated (or Jmol has chosen by default) for the color range from one
end to the other of the color scheme. Is it reporting something different
than you expect?
> If I want to set an actual range in Jmol script, are the actual atomic
> charges the values that I should use as my guide?
>
>
very good question. I don't have an answer to that. Personally I think a
standard range is best - but for cations or anions you might want to
consider something different. Realize that you can know the overall charge
(roughly) with
Var overallCharge = {*}.partialcharge.sum
and you can also use
{*}.partialcharge.min
{*}.partialcharge.max
if you think that would be helpful.
>
>
>
> Right now, Jmol 11 ignores any charges on atoms more than 8 angstroms away
> from a given point, which doesn't mean much for small models. More
> significantly, though, Jmol right now creates a "field" of potential around
> the model and then uses that to map the surface. This isn't really necessary
> -- you can just pick a surface point and sum all the q/d from all the atoms.
> I've just rewritten the code for 12.0 and 12.1 to do that and will get that
> in the next release.
>
> Related to this, I'm not sure that I understand varying Jmol surface
> dimensions. Am I correct that these are the options for creating a surface
> to map?
>
> 1) Solvent
> 2) Molecular
> 3) van der Waals at settable % values
>
> The reason that I ask this is that Spartan creates something called a bond
> surface map, and I'm trying to translate that into Jmol thinking.
>
>
There are two basic surface types -- ones that are basically the connection
of spacefill spheres (vdw, sasurface), and ones that round out the sharp
edges of those (molecular, solvent).
1) Solvent is probably not something you are interested in. It ignores H2O
and then does a molecular surface at the VDW radii and rounded using the
setting of solventProbeRadius.
2) Molecular is a nice option -- rounds out the VDW sphere connections using
a rolling ball of radius 1.4 Angstroms.
3) VDW -- most adjustable; all sorts of options.
4) sasurface x -- just a subset of VDW (vdw +x, or solventProbeRadius for
default), but also -- like solvent -- ignores H2O.
Solvent and sasurface are more for biomolecular surfaces, not small
molecules.
So your best options are (2) and (3). Molecular is a bit prettier; VDW is
more adaptable.
Bob
--
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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