Thanks to everyone for helping with this.  I understand where I was going wrong and I've got things in much better shape now.  I have another question.  I've pulled data out of the file loaded into Jmol and used it to plot points in an svg element.  I would like to use jQuery to access those points which all have class="circle".  Here is the code:

$(".circle").click(function(){
circle_click(evt);
});

This does nothing.  Similar code works fine to access other elements on the page, just not in the svg.  The circle_click(evt) works when I place an onclick="circle_click(evt)" within the tag for the circle element in the svg.


***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhansen@depauw.edu
***********************************************


On May 27, 2009, at 4:37 PM, Robert Hanson wrote:

Jeff, I'm using jQuery at

http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot.htm

and

http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm

I'm sure your problems do not arise from Jmol.js. The jQuery business is quite well modularized.

Bob



On Wed, May 27, 2009 at 11:04 AM, Andreas Prlic <andreas@sdsc.edu> wrote:
Hi Jeff,

Now sure what's exactly the problem from your description, perhaps you
can send some example code?

We are using a mix between JQuery and self written javacript on the
new RCSB-PDB web site:

e.g. this page tracks the Jmol console output to a div and shows the
command history:
http://www.rcsb.org/pdb/explore/jmol.do?structureId=1CDG

This page maps sequence domains on the structure:
http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=1CDG&params.showJmol=true

Andreas



On Wed, May 27, 2009 at 8:11 AM, Jeff Hansen <jhansen@depauw.edu> wrote:
> Does anyone have any experience using jQuery on a page with Jmol?  I
> wanted to do this as it would greatly simplify some things I wanted to
> do.  Unfortunately, none of the jQuery seems to be working.  Let me
> explain.  I can load a Jmol applet and structure and write javascript
> to manipulate it in different ways but any calls to jQuery functions
> simply do not execute.  When I played around with jQuery on a simple
> test page (without Jmol) it was fine.  If anyone can help with this I
> would really appreciate it.  My alternative is to return to some
> kludgy code and I'd rather not.
>
> ***********************************************
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhansen@depauw.edu
> ***********************************************
>
>
>
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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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