X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=b1ad4bae86c77cc534a3285c370a2a3e864cb54e;hb=383fd91269f510b189450fbe174e9c051103c7eb;hp=c5c4d093f87bd36b610a5c479c09db1517eccdd7;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index c5c4d09..b1ad4ba 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 Structures</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.
@@ -68,49 +69,51 @@
         <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>
+    <img src="schooser_viewbutton.png"
+      style="width: 465px; height: 81px" /><br/> <strong><a
+      name="afterviewbutton">Controlling where the new structures
+        will be shown</a></strong>
+        <br />The Structure Chooser offers several options
+    for viewing a structure. <br/><strong>New View</strong> will open a new
+    structure viewer for the selected structures, but if there are views
+    already open, you can select which one to use, and press the <strong>Add</strong>
+    button. Jalview can automatically superimpose new structures based
+    on the linked alignments - but if this is not desirable, simple
+    un-tick the <strong>Superpose Structures</strong> checkbox.
 
+  </p>
   <p>
-    If a <strong>single</strong> PDB structure is selected, one of the
-    following will happen:
+    <em>Superposing structures</em><br/>Jalview superposes structures using
+    the visible portions of any associated sequence alignments. A
+    message in the structure viewer's status bar will be shown if not
+    enough aligned columns were available to perform a superposition.
   </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
-    </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for
-      more information about the display.
-    </li>
-  </ul>
-
+  <p>
+  See the <a href="jmol.html">Jmol
+    </a> and <a href="chimera.html">Chimera</a> help pages for
+      more information about their capabilities.</p>
+  
 
   <p>
     <strong>Retrieving sequences from the PDB</strong><br>You can
