Merge branch 'develop' into features/JAL-250_hideredundantseqs

[jalview.git] / help / html / features / viewingpdbs.html

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index f60da1a..0fcbbf9 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -76,14 +76,12 @@
       </ul></li>
   </ol>
   <p>
-  <strong>Structure Viewers in the Jalview Desktop</strong><br/>
-  The
-  <a href="jmol.html">Jmol viewer</a> has been included since Jalview
-  2.3. Jalview 2.8.2 included support for
-  <a href="chimera.html">Chimera</a>, provided it is installed and can
-  be launched by Jalview. The default viewer can be configured in the
-  <a href="preferences.html#structure">Structure tab</a> in the
-  <strong>Tools&rarr;Preferences</strong> dialog box.
+    <strong>Structure Viewers in the Jalview Desktop</strong><br /> The
+    <a href="jmol.html">Jmol viewer</a> has been included since Jalview
+    2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>,
+    provided it is installed and can be launched by Jalview. The default
+    viewer can be configured in the <a href="preferences.html#structure">Structure
+      tab</a> in the <strong>Tools&rarr;Preferences</strong> dialog box.
   <p>
     Structure data imported into Jalview can also be processed to
     display secondary structure and temperature factor annotation. See
@@ -97,12 +95,15 @@
     whether structure views already exist for the selected structures or
     aligned sequences.
   </p>
+  <p>If multiple structures are selected, then Jalview will always
+    create a new structure view. The selected structures will be
+    imported into this view, and superposed with the matched positions
+    from the aligned sequences. A message in the structure viewer's
+    status bar will be shown if not enough aligned columns were
+    available to perform a superposition.</p>
   <p>
-    If multiple structures are selected, then Jalview will always create
-    a new structure view. The selected structures will be imported into
-    this view, and superposed with the matched positions from the
-    aligned sequences.<br /> If a <strong>single</strong> PDB structure
-    is selected, one of the following will happen:
+    If a <strong>single</strong> PDB structure is selected, one of the
+    following will happen:
   </p>
 
   <ul>
@@ -111,10 +112,9 @@
 
     <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"></a> to
-    the structure in the existing view. (<em>new feature in Jalview
-      2.6</em>).
-  </li>
+      href="jmol.html#align"></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