git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
JAL-1517 update copyright to version 2.8.2
[jalview.git] / help / html / features / viewingpdbs.html
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 6c10e98..412a23a 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -24,8 +24,31 @@
 <p><strong>Viewing PDB Structures</strong></p>
 
 <p>Jalview can view protein structures associated with a sequence
-via the <strong>"Structure&rarr;View PDB entry:"</strong> entries from a
-sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Once a pdb
+via the <strong>"Structure&rarr;"</strong> submenu from a
+sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.</p>
+<p>The following menu entries are provided for viewing structure data<br>
+  <ul>
+    <li>The <strong>&quot;Structure&#8594;View
+        Structure&#8594;</strong> submenu allows a single PDB structure to be chosen
+      for display from the available structures for a sequence.
+    </li>
+    <li>The <strong>&quot;Structure&#8594;View all <em>N</em>
+        structures
+    </strong> option will open a new window containing all structures associated
+      with the current selection, superposed according to the currently selected region of the alignment.<br/><em>This
+      capability was added in Jalview 2.7</em>
+    </li>
+    <li><a name="viewreps"/>The <strong>&quot;Structure&#8594;View all <em>N</em>
+        representative structures
+    </strong> option will open a new window containing exactly one structure per
+      currently selected sequence.<br />
+    <em>The View representative structures option was introduced in
+        Jalview 2.8.1</em></li>
+  </ul>
+  <br> 
+</p>
+
+<p>If a single pdb
 structure is selected, one of the following will happen:</p>
 
 <ul>
@@ -44,17 +67,6 @@ structure is selected, one of the following will happen:</p>
        <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>&rarr;</strong> Associate Structure with