Let us know how that works with Sun Java. I'm not seeing any problem. But I
do note that by using the applet tag you are not properly registering the
applets within the JmolAppletRegistry, which allows communication among
applets. Please see if the problem persists while using Jmol.js. If you want
to have the script just lines of text, you can do so on the page as follows:
<!--
/** **** Jmol Embedded Script ****
[script text here]
**/
-->
<script language="javascript" src="Jmol.js"></script>
<script language="javascript">
jmolInitialize("./jmol", "JmolApplet.jar")
jmolApplet(400,'script "' + document.location + '" ')
</script>
I seems to me introducing a modicum of JavaScript should be a plus, not a
minus, for your students.
On Thu, Nov 12, 2009 at 9:58 AM, Kevin Cowtan <[email protected]>wrote:
> I've been experimenting with driving Jmol from a psp webapp as part of a
> programming assessment which I am setting. In the process of doing this,
> I've run into an instability in Jmol 11.9.8 and 11.8.9.
>
> I also tried 10.2.0, which was rock solid.
>
> I'm using Firefox 3.0.15 on Fedora 10. I now see that I am using the
> IcedTea Java plugin with comes with Fedora, rather than an official Sun
> Java. That is most probably the cause of the problem, but I guess I'll
> send this anyway in case it is useful for future reference. Safari works
> fine on the same pages.
>
> I include links to two copies of an auto-generated page (which contains
> a rather long applet string specifying the colour of each residue
> inidivualy in a large protein) and PDB file. The two copies differ in
> which version of Jmol is being used.
>
> Reloading the Jmol 11.* page a few times leads to the browser
> functionality gradually locking up - typically on the first load the
> context menu on the page body stops working, on the subsequent reloads
> the browser menus stop working, and eventually the browser freezes
> completely (although the Jmol applet is still working).
>
> No such problems are seen with Jmol 10.*
>
> Here are the pages:
> http://www.ysbl.york.ac.uk/~cowtan/jmol11/residues_by_chain.psp.html<http://www.ysbl.york.ac.uk/%7Ecowtan/jmol11/residues_by_chain.psp.html>
> http://www.ysbl.york.ac.uk/~cowtan/jmol10/residues_by_chain.psp.html<http://www.ysbl.york.ac.uk/%7Ecowtan/jmol10/residues_by_chain.psp.html>
>
> I haven't tried any of this using jmol.js. We're teaching
> python rather than Java or JavaScript, so I am trying to avoid confusing
> the students with other general purpose languages, hence using the
> Rasmol input.
>
> Hope that helps,
> Kevin Cowtan
>
>
>
>
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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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