Hello, Vincent

> I'm planing to integrate JMol to my application to view PDB files and  
> ligand pockets. Basically, my pockets will be represented by several  
> spheres placed in the structure (input as PQR format)

You can read PQR files into Jmol without problem, can't you?


> My question would be: is there any way to get the Jmol popup menu that  
> one get when right clicking on the desktop version of Jmol ?

I'm not sure I understand you fully.
The applet has the same popup menu as the application, except for file 
operations (due to 
Java security restraints). You can use the signed applet to have those too.

Ah, I see. You mean having the menu in your custom application. I cannot help 
on that.

> And more generally, what is the best and most recent place to learn  
> how to integrate Jmol into an application? I'm currently using  
> Biojava's examples, and I've checked the Jmol wiki here:
> http://wiki.jmol.org/index.php?title=Applications_Embedding_Jmol

Don't think there's any doc for that.Maybe others that have development 
experience can 
help you there.

Good luck!


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