I believe my problem is with relative/absolute file pathing.
What is unclear to me is the following:
Given I can load an applet, and from its "Main" menu, I open the 
console. In the console i hit "cd", showing me the "default directory". 
What is the definition of "default directory"?
Say "cd" prints

www.thisjmolpage.com

to the console and I use a Jmol script to set up the applet. Any path in 
the Jmol script has to be relative to this path, correct? Or relative to 
the HTML document initializing the Jmol applet?

Thanks for any clearification.





On 13.04.12 12:28, Jaime Prilusky wrote:
> A server side script should work fine. Can you provide a URL to see what you 
> get?
>
> Jmol + server side scripts that generate HTML on the flight are used on 
> numerous sites. A few examples
>
> http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CTS
>
> http://oca.weizmann.ac.il/oca-bin/ccpeek?id=2CTS
>
> http://www.proteopedia.org/wiki/index.php/1stp
>
> Jaim
>
> On Apr 13, 2012, at 11:17 AM, Martin Hediger wrote:
>
> Dear Jmol Users
> I'm running a website, where a server side script carries out a number
> of steps, builds up a new HTML structure including a Jmol applet and
> returns it to the browser to be displayed. Without the jmolApplet call,
> everything builds up nicely, but using jmolApplet([300,300]), the page
> is overwritten and only the applet displays.
>
> What are common reasons for such behaviors?
> Thanks for any feedback.
> Martin
>
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