oh, yes! You can do all that. Check the Jmol wiki for lots of tips. Commands
include jmolEvaluate (my favorite), and jmolGetPropertyAsArray() or
jmolGetPropertyAsString()
On Thu, Aug 21, 2008 at 12:41 AM, Jeff Hansen <[EMAIL PROTECTED]> wrote:
> Thanks Bob. That certainly works. So basically anytime I want to pull out
> some info from the molecule file I need to do that in the jmolApplet
> command. Or is there a way to do that prior to loading the molecule into
> Jmol? I'm looking ahead to situations where I'll want to dynamically load a
> structure into an applet, grab some data out of it and do some stuff with
> it. Now I'm wondering how I'll be able to update other parts of the web
> page based on this data if the applet hasn't finished loading the file yet.
> Is there a way to find out what properties are accessible from the applet?
> I'm looking at getting a protein's sequence into an array or a small
> molecule's energy. If these aren't directly accessible can the entire file
> be brought into a string variable and then dig the info out of it?
>
> Thanks again.
>
>
> ***********************************************
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> [EMAIL PROTECTED]
> ***********************************************
>
>
> On Aug 20, 2008, at 3:43 PM, [EMAIL PROTECTED]:
>
> Message: 4
> Date: Wed, 20 Aug 2008 14:42:00 -0500
> From: "Robert Hanson" <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] getting info from Jmol applet
> To: [email protected]
> Message-ID:
> <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Jeff,
>
> The mistake here is timing. You cannot query an applet while the page is
> loading (prior to </body> and completion of applet initialization). In some
> cases this crashes browsers; in others it just causes an error; in others
> it
> permanently disables the applet communication.
>
> The simple fix is to place the JavaScript code in a function defined in the
> <head> block, and then add a JavaScript call to that function in the
> start-up Jmol script, after the file is loaded. No need for form tags.
>
> <head>
> <script type="text/javascript">
> function appletReady() {
> var atomSetArray = jmolGetPropertyAsArray("atomInfo","atomno<5");
> alert (atomSetArray[0].info);
> }
> </script>
> </head>
> <body>
> <script type="text/javascript">
> jmolInitialize("jmol");
> jmolApplet(500, "load ../Jmol/jmol/models/1bf3.pdb;javascript
> appletReady()");
>
> </script>
>
> </body>
>
>
>
>
>
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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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