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
[email protected]
http://chemagic.org
> On Jun 7, 2016, at 5:39 AM, Krishna Mohan <[email protected]> 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
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
> patterns at an interface-level. Reveals which users, apps, and protocols are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
