I also have a version of the panel that makes use of SimpleViewer.

And now it's working o_O, I have the popup menu triggered at right  
clic. Here is the code:

public class JmolPanel extends JPanel
{
     private static final long serialVersionUID = -3661941083797644242L;

     private JmolSimpleViewer viewer;
     private JmolAdapter adapter;

     public JmolPanel() {
         adapter = new SmarterJmolAdapter();
         viewer = JmolSimpleViewer.allocateSimpleViewer(this, adapter);
     }

     public JmolSimpleViewer getViewer() {
         return viewer;
     }

     public void executeCmd(String rasmolScript) {
         viewer.evalString(rasmolScript);
     }

     public void setStructure(Structure s)
     {
         String pdb = s.toPDB();
         viewer.openStringInline(pdb);
     }

     final Dimension currentSize = new Dimension();
     final Rectangle rectClip = new Rectangle();

     @Override
     public void paint(Graphics g) {
         getSize(currentSize);
         g.getClipBounds(rectClip);
         viewer.renderScreenImage(g, currentSize, rectClip);
     }
}

I'm quite dubitative though, I don't understand why it didn't worked  
previously as it was the first tryout, and I think it was quite the  
same piece of code...

Anyway, the previous code that makes use of the Viewer class directly  
is not working cauz there is a nullpointerException thrown when right  
clicking on the panel:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
         at org.jmol.viewer.Viewer.getSelectionHaloEnabled(Unknown Source)
         at org.jmol.viewer.Viewer.getBooleanProperty(Unknown Source)
         at org.jmol.viewer.Viewer.getBooleanProperty(Unknown Source)
         at org.jmol.popup.JmolPopup.show(Unknown Source)
         at org.jmol.viewer.Viewer.popupMenu(Unknown Source)
         at org.jmol.viewer.MouseManager.mousePressed(Unknown Source)
         at org.jmol.viewer.MouseManager11.mousePressed(Unknown Source)

Anyway, I think I have what I need for the moment, thank you very much  
for your help. No doubt I will come back soon for more information on  
customizing all these stuffs :)

Thanks again.
Vincent.



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