Reinhold,
Jmol won't assume those temperature values are partial charges. So what
you have to do is assign the partial charges yourself based on that
data. The way this is done is really quite easy in 11.4 (not 11.2):
{*}.partialCharge = {*}.temperature.all
That assigns the partial charges based on the list of temperature
values. Then, after that, you can use
isosurface sasurface map mep
for example. I notice that the popup menu doesn't reconfigure to show
the MEP option, but that will be fixed.
Bob
Reinhold Stoermann wrote:
>Hello to all,
>
>I just joined this list, because I currently try to convert a website
>from using the old MDL Chime to jmol.
>(jmol 11.2.14).
>
>The molecules are represented by a bunch of PDB files, where the columns
>61-66 usually holding the temperature factor have been filled instead
>with partial charges of the atoms which where computed with MOPAC.
>
>This arrangement made it possible in Chime to generate an isosurface
>with a coloring scheme according to the partial charges.
>
>If I laod the same pdb files in jmol, the menu option
>
>Surfaces -> Molecular Electrostatic Potential
>
>is not accessible, and a script using the command
>
>color atoms temperature
>
>gives an image of red an blue atom colorings bearing no relation to the
>"temperature factors" (which are actually partial charges). Even if I
>change some of the these values in the pdb file by hand, this has no
>effect on the given coloration of the manipulated atoms.
>
>Maybe Jmol does not support this trick to visualize molecular
>electrostatic potentials from pdb files?
>
>So if I have to convert the pdb files to some other format, what would
>it be?
>(I still need the pdb columns for the "residue name" to be conserved in
>that other format, because some other coloration scheme depends on that.)
>
>
>Dr. Reinhold Störmann
>Bioorganic Chemistry
>Center for Environmental Research & Technology (UFT)
>Leobener Str.
>D-28359 Bremen
>
>
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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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