code: public static void showMultipleAligmentPanel(MultipleAlignment multAln,
  			AbstractAlignmentJmol jmol) throws StructureException {
  
  		MultipleAligPanel me = new MultipleAligPanel(multAln, jmol);
  		JFrame frame = new JFrame();
  
  		frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
  		frame.setTitle(jmol.getTitle());
  		me.setPreferredSize(new Dimension(
  				me.getCoordManager().getPreferredWidth() ,
  				me.getCoordManager().getPreferredHeight()));
  
  		JMenuBar menu = MenuCreator.getAlignmentPanelMenu(
  				frame,me,null, multAln);
  		frame.setJMenuBar(menu);
  
  		JScrollPane scroll = new JScrollPane(me);
  		scroll.setAutoscrolls(true);
  
  		MultipleStatusDisplay status = new MultipleStatusDisplay(me);
  		me.addAlignmentPositionListener(status);
  
  		Box vBox = Box.createVerticalBox();
  		vBox.add(scroll);
  		vBox.add(status);
  		frame.getContentPane().add(vBox);
  
  		frame.pack();
  		frame.setVisible(true);
  
  		frame.addWindowListener(me);
  		frame.addWindowListener(status);
  	}
docs: Creates a new Frame with the MultipleAlignment Sequence Panel.
  The panel can communicate with the Jmol 3D visualization by
  selecting the aligned residues of every structure.
  
  @param multAln
  @param jmol
  
  @throws StructureException