OK, I see how to do this. 1) transform your data into what looks like an XYZ file, where the first part is the actual atoms, and the second part is as set of "bogus" atoms positioned where you need them and including the data you want to plot in the fifth column. I made a little .xyz file using Excel. But you could do it with Jmol scripting as well. The file looks like this:
227
C -0.199999 -0.309948 -0.463554
C 1.328281 -0.309948 -0.463554
C 1.829054 1.110428 -0.463554
C -0.729241 -1.734088 -0.479755
Cl 3.716621 0.988878 -0.443163
H -0.588478 0.23564 0.422575
H -0.588776 0.255435 -1.337048
H 1.723662 -0.86262 0.415297
H 1.724508 -0.861985 -1.342402
H 1.593678 1.690312 -1.36857
H 1.574928 1.697606 0.431649
H -1.828714 -1.759592 -0.479517
H -0.401381 -2.291613 -1.36905
H -0.400229 -2.311819 0.396145
Xx -1.033075 1.479272 -0.28151 -0.001523
Xx -2.098453 0.197779 -0.866198 0.000799
Xx -1.501445 1.182288 -0.589701 -0.001548
Xx -1.991341 0.484824 -0.769458 -0.000396
...
etc.
...
2) load that file.
3) set VDW radii.
4) create an isosurface for the atoms and color it by the partial charge
data in the segment data.
5) delete the unwanted "atoms" (segment positions).
Here's the script:
load t.xyz
{_H}.vdw = 1.416
{_C}.vdw = 2.006
{_Cl}.vdw = 2.365
isosurface select {not _XX} ignore {_XX} solvent 1.2 map select {_XX} ignore
{not _XX} property partialcharge colorscheme "rwb"
delete _XX
I think that's about as good as you can do. Could be interesting to
streamline this and allow mapping of any such point-based data. Have to
think about that....
Bob
On Sat, Feb 19, 2011 at 5:31 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> These just use the coordinates from
>
> load $1-chlorobutane
>
> Presumably you have a model in some other file, right?
>
> I see this in the file:
>
> EPS=999.0 COSWRT RSOLV=1.2 RM1 NSPA=92
> VDW(;H=1.416;C=2.006;N=1.829;O=1.7936;F=
> 1.7346;S=2.124;P=2.124;CL=2.365;BR=2.183;I=2.3364) GNORM=0.1 RELSCF=0.1
>
> OK, I think I see part of what you are after, sort of. I plotted the points
> in the SEGMENT section, and they appear to be points on a VDW surface. Jmol
> can reproduce that surface using
>
> load $1-chlorobutane
> {_H}.vdw = 1.416
> {_C}.vdw = 2.006
> {_Cl}.vdw = 2.365
> isosurface solvent 1.2
>
> and every point is on it. Note, by the way, that this is NOT a
> solvent-accessible surface; it's a solvent-excluded surface.
>
> Q: Is that what you expected -- solvent-excluded, not solvent-accessible?
>
> Q: These are rather unusual Van der Waals radii. Where do they come from?
> Jmol by default uses H=1.1, C = 1.7, Cl 1.75. Why are these VDW radii so
> large?
>
> Q: How does a "segment" have only a point (and not, perhaps, three points)
> and still have an "area"?
>
> Q: I see the COSMO-CHARGE column is basically all zeros. What is the
> significance of the SIGMA column?
>
> I don't have access to Perkin Transactions, so I need your help
> understanding the purpose of these values.
>
>
But, basically, I think what you want to do is create a surface that is
based on values at those points. What we need are triangles, not points.
Nothing here gives any clue as to how to connect those dots into triangles?
Jmol doesn't do that by itself. I suppose we could write something that does
that, but
--
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
<<attachment: t.jpg>>
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