one last thing -- with the latest Jmol you can do:
load xxxx.pdb
{*}.partialcharge = data(load("whatever.mol2"),9,0,9)
All in one swoop, you have your partial charges.
That loads file whatever.mol2 into a temporary variable, then takes the 9th
field* starting at the 9th line. Using "9,0,1" there would also work,
because there are fewer than 9 fields in all the lines preceding the atom
lines, but it's better, I think, to indicate the true starting line in case
some file has a long title.
*The 0 there indicates this is a free-format file and we are indicating the
9th white-space-separated field on the line; if it had been a fixed-format
file, then the first numeric parameter would indicate a column number, and
the 0 would be replaced with the number of columns for this field.
Bob
On Sun, Sep 21, 2008 at 10:17 AM, Reichsman Frieda <[EMAIL PROTECTED]>wrote:
>
> On Sep 19, 2008, at 10:12 PM, Robert Hanson wrote:
>
> >
> > The way to get partial charge data into .pdb files is to put it in
> > the temperature field. You can do that with:
> >
> > {*}.temperature = {*}.partialcharge.all
> >
> > Which will work on the revised Jmol that I haven't uploaded yet.
> >
> > Which suggests to me that you might also try this in the version you
> > have:
> >
> > {*}.partialcharge = {*}.property_partialcharge.all
> >
> > That copies all the property_partialcharge data into the real
> > partialcharge field of the atoms.
> >
> > Then do the isosurface MEP business.
>
>
> Yes, this works perfectly for displaying the mep surface- beautiful!
> And being able to get the values into the pdb file will be terrific.
>
> Thanks,
> Frieda
>
> > On Sep 13, 2008, at 1:00 PM, Robert Hanson wrote:
> >
> >> If that's all you want to do, try this:
> >>
> >> load "xxxx.pdb"
> >> set propertydatafield 9
> >> x = load("xxxx.mol2")
> >> data "property_partialcharge @x"
> >> color property_partialcharge
> >>
> >>
>
>
> //////////////////////////////////////
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
> 413-253-2405
>
> //////////////////////////////////////
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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