Right, you could include it as an embedded
jmolscript: ......
in the line2 comment
On Fri, Nov 13, 2009 at 10:19 PM, Joe Gatewood <[email protected]> wrote:
> Bob,
>
>
>
> I looked at the xyz reader code and do not think I can accomplish what I
> had in mind.
>
>
>
> My goal was to include the color and radius values in the atom definition
> line so they got set during model reading. In this use case the number of
> atoms is not that large so I will just set the color and size after all the
> atoms have been loaded and I know their indice.
>
>
>
> Thanks,
>
> Joe
>
>
>
>
> ------------------------------
>
> *From:* Robert Hanson [mailto:[email protected]]
> *Sent:* Friday, November 13, 2009 8:44 PM
> *To:* [email protected]
> *Subject:* Re: [Jmol-developers] set atom color/radius on load
>
>
>
> Not sure what "during load" refers to, but
>
> label %4.0[color] %3.2[vdw]
>
> gets you rgb colors and van der Waals radii.
>
> label %4.0[color] %3.2[radius]
>
> gets you the same with instead the current spacefill radius
>
> you can set the atom color using a script:
>
> {atomindex=1}.color = "[xFF00FF]"
> {atomindex=2}.color = "red"
> {atomindex=1}.color = "[128 0 128]"
>
> that sort of thing. Similarly, you can set radii using, for example,
>
> {atomindex=33}.radius = 2.0
>
>
>
> Bob
>
> On Thu, Nov 12, 2009 at 2:19 PM, Joe Gatewood <[email protected]> wrote:
>
> I have spent some time looking for the syntax to use to set the color and
> radius of an individual atom at load time.
>
> For example in one of my use cases I am building up the model one atom at a
> time and loading using evalScript("|K 10 3 20|...")
> Can I set the color and radius of each atom as part of the atom descriptor?
>
> I enjoyed the web content (discussion) on Jmol colors. I can set the color
> with select fine but did not find documentation on setting single atom
> color
> during load.
>
> Thanks,
> Joe
>
>
>
>
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>
>
> --
> 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
>
>
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--
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
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