Sort of a "characature" of ESP. I doubt anyone has tried this. The quick
answer is "sure, that's possible." What you do is map atomic charge to
atomic radius. It's pretty straightforward. Something like:
var myscale = 3
{*}.radius = {*}.partialcharge.all.mul({*}.partialcharge.all).mul(myscale)
that bit on the right makes a list of partial charges and squares them, so
that you don't have negative radii. If that's too drastic and nonlinear, a
slightly more involved script could give just absolute values. By equating a
property on the left with a list on the right, we assign all values at once.
Then
color {*} property partialcharge
Now, if you want a surface, then instead of radius you use van der Waals:
{*}.vdw = {*}.partialcharge.all.mul({*}.partialcharge.all)
and then use
isosurface sasurface 0
to request a solvent-accessible surface with a probe radius of 0 Angstroms
-- i.e. at the VDW radius, which we have just defined in this curious way.
Could be interesting...
Bob
On Mon, Sep 7, 2009 at 1:38 PM, Jeff Hansen <[email protected]> wrote:
> Everyone,
>
> I was talking with a colleague earlier today about nucleophiles and
> electrophiles and how to visualize these in modeling programs. Of
> course one could map electrostatic potential onto a surface. Often
> times it is difficult though to clearly see where the nucleophilic and
> electrophilic sites are in the molecule. We were wondering if it
> might be possible to not only map a color to the surface but also
> adjust the size of the surface according to electrostatic potential.
> In other words, the higher the potential the further the surface
> extends from the nucleus up to a limit of the Van der Waals radius.
> Thus an electrophilic site would not only be appropriately colored,
> but it would also be larger than sites with little potential and the
> same for nucleophilic sites.
>
> So has anyone ever seen something like this? Would it be possible?
> Would it even be desirable or is this something better left not done?
>
>
> Jeff
>
>
> ***********************************************
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> [email protected]
> ***********************************************
>
>
>
>
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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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