-<p>Jalview can view protein structures associated with a sequence via the <strong>"Structure→View
- PDB entry:"</strong> entries from a sequence's <a
- href="../menus/popupMenu.html">pop-up menu</a>. This will open an
- interactive display of the structure in a new window, or prompt you
- to associate the sequence with an existing view of the selected
- structure. See the <a href="jmol.html">Jmol PDB viewer</a> help page
- for more information about the display.
-</p>
-<p>To associate PDB files with a sequence, right click on a sequence ID and select
- "Structure<strong>→</strong> Associate Structure with Sequence",
- and one of the submenus:</p>
+
+<p>Jalview can view protein structures associated with a sequence
+via the <strong>"Structure→View PDB entry:"</strong> entries from a
+sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Once a pdb
+structure is selected, one of the following will happen:</p>
+
+<ul>
+ <li>If no structures are open, then an interactive display of the
+ structure will be opened in a new window</li>
+
+ <li>If another structure is already shown for the current
+ alignment, then you will be asked if you want to add and <a
+ href="jmol.html#align">align this structure</a> to the structure in
+ the existing view. (<em>new feature in Jalview 2.6</em>)</li>
+
+ <li>If the structure is already shown, then you will be prompted
+ to associate the sequence with an existing view of the selected
+ structure. This is useful when working with multi-domain or multi-chain PDB files.</li>
+
+ <li style="list-style: none">See the <a href="jmol.html">Jmol
+ PDB viewer</a> help page for more information about the display.</li>
+</ul>
+ <p>
+ <em>Opening structures associated with the current selection</em><br />
+ If one or more of the sequences in the alignment are selected, then
+ the Structure submenu of the <a href="../menus/popupMenu.html">Sequence
+ ID popup menu</a> will contain will include either a 'View all <em>X</em>
+ structures' entry in the submenu or a 'View structure for <em>Sequence</em>'
+ entry. Both these options will open a new Jmol view containing one, or
+ all the structures available for all selected sequences, superimposed
+ using the currently selected region of the alignment. (<em>This
+ capability was added in Jalview 2.7</em>)
+ </p>
+ <p><strong>Associating PDB files with Sequences</strong></p>
+ <p>To associate PDB files with a sequence, right click on a sequence
+ID and select "Structure<strong>→</strong> Associate Structure with
+Sequence", and one of the submenus:</p>
+