-has been integrated into Jalview. It is automatically used by the\r
-application, and should also run in the applet in all latest web\r
-browsers. If jmol is not available, then the original <a\r
-href="pdbviewer.html">internal pdb viewer</a> will be used as a fallback.\r
+has been integrated into Jalview for interactively viewing structures\r
+opened by selecting the <strong>"Sequence→View PDB\r
+entry:"</strong> option in the <a href="../menus/popupMenu.html">sequence\r
+id pop-up menu</a> (if you can't see this, then you need to <a\r
+ href="viewingpdbs.html">associate a PDB structure</a> with the\r
+sequence). Jmol is available from the Jalview desktop and should also\r
+run in the JalviewLite applet, providing the browser supports Java 1.5.\r
+If Jmol is not available, then the original <a href="pdbviewer.html">internal\r
+pdb viewer</a> will be used as a fallback.</p>\r
+<p><a name="align"><strong>Superposing structures based\r
+on their aligned sequences</strong></a><br>\r
+If several structures are available on the alignment, you may add\r
+additional structures to an existing Jmol view by selecting their entry\r
+in the appropriate pop-up menu. Jalview will ask you if you wish to add\r
+the structure to the existing alignment, and if you do, it will import\r
+and superimpose the new PDB file using the corresponding positions from\r
+the alignment. If the alignment is subsequently edited, you can use the\r
+<a href="#sAlign"><em>Jmol→Align</em></a> menu option from the\r
+menu bar of the structure view window to superpose the structures using\r
+the updated alignment.<br>\r
+<em>Sequence based structure superposition was added in Jalview 2.6</em>\r