I just tried this using methylfluoride.smol. If I just do isosurface
sasurface 0 map mep I get what you would expect. If I do
{*}.vdw = {*}.partialcharge.all.mul({*}.partialcharge.all)
isosurface sasurface 0 map mep
I don't get what I hoped for. When I then do print {*}.vdw it returns
a single value of 0.06260959.
Any ideas what I'm doing wrong here?
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[email protected]
***********************************************
On Sep 7, 2009, at 5:52 PM, Robert Hanson wrote:
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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