Km,
Providing that Jmol is reading those partial charges, you can use the following
script:
color {*} partialCharge
If Jmol does not read the charges in an XYZ, MMFF94 charges can be calculated.
The script becomes;
calculate partialCharge; color {*} partialCharge
With the above, I think you are limited the red-white-blue color gradient.
If you want to assign your own colors by hand, then in a XYZ file you can add a
script line to the unused second line of the XYZ file:
jmolscript: select {atomno = 1}; color red; select {atomno = 2}; color pink; etc
The jmolscript: above is part of this second line.
Here is a useful Jmol color chart:
http://www.biorom.uma.es/contenido/biomodel/Jmol/colors/jmol_colors.en.htm
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jun 7, 2016, at 5:39 AM, Krishna Mohan <krishna.mo...@mbcet.ac.in> wrote:
>
> Dear list
>
> In order to color different partial charges for each and every atoms in a XYZ
> file (, as shown in the below format)
>
> . . .
> atom x y z <partial charges>
> . . .
>
> I would like to know, how a jmol script can be written to assign a particular
> color for Each atom ?
> I.e., suppose if I have 2 atoms, how can I assign the color for,
>
> h 1.0000 1.00000 1.00000 [[48,80,248] or 3050F8]
> h 0.0000 0.00000 0.00000 [[80,208,80] or 50D050]
>
> etc., so that One can see the variation of partial charges for individual
> atoms.
>
> Hope someone can help
>
> thanks in advance
>
> Km
>
>
>
>
>
>
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