X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=0fcbbf9290360fcfe3d5346c8490e0277f93be0c;hb=c350f93c6fac69b6a8a65645f0e89e26451df146;hp=c5c4d093f87bd36b610a5c479c09db1517eccdd7;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index c5c4d09..0fcbbf9 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -53,11 +53,12 @@
       'highest resolution', simply choose another to pick structures in
       a different way.<br />
       <ul>
-        <li><strong>Viewing Cached Structures</strong><br />If you
-          have previously downloaded structures for your sequences, they
-          can be viewed by selecting the <strong>Cached PDB
-            Entries</strong> option from the drop down menu at the top of the
-          dialog box.</li>
+        <li><strong>Viewing Cached Structures</strong><br />If
+          previously downloaded structures are available for your
+          sequences, the structure chooser will automatically offer them
+          via the <strong>Cached PDB Entries</strong> view. If you wish
+          to download new structures, select one of the PDBe selection
+          criteria from the drop-down menu.</li>
       </ul></li>
     <li><strong>To view selected structures, click the <strong>"View"</strong>
         button.
@@ -68,23 +69,38 @@
         <li><a href="siftsmapping.html">SIFTS</a> records will also
           be downloaded for mapping UniProt protein sequence data to PDB
           coordinates.</li>
+        <li>A new structure viewer will open, or you will be
+          prompted to add structures to existing viewers (see <a
+          href="#afterviewbutton">below</a> for details).
+        </li>
       </ul></li>
   </ol>
-
-  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>
+    <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
     the <a href="xsspannotation.html">Annotation from Structure</a> page
     for more information.
   </p>
-
+  <p>
+    <strong><a name="afterviewbutton">After pressing the
+        'View' button in the Structure Chooser</a></strong><br /> The behaviour of
+    the 'View' button depends on the number of structures selected, and
+    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 a <strong>single</strong> PDB structure is selected, one of the
     following will happen:
@@ -96,8 +112,8 @@
 
     <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>).
+      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
