print {*}.xxx
gets you an average.
print {*}.xxx.all
gets you a list.
Or you can use
label %[vdw]
to view them as labels
On Tue, Sep 8, 2009 at 11:00 PM, Jeff Hansen <[email protected]> wrote:
> 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.
>
what do you get?
> 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]
>> ***********************************************
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> 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
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.
> http://p.sf.net/sfu/bobj-july_______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
