X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=4904856d1fd311df7aa55befe18eeedad3c17fb6;hb=e66bdc1c0086ab56c56979d9dc6635e81503eb84;hp=679f35303af73c34f709b32761589352d37c64b0;hpb=793968f15efc19ba0b8a91b0078e6b23ee4e2ff9;p=jalview.git

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 679f353..4904856 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,14 +1,14 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -38,22 +38,23 @@ structure is selected, one of the following will happen:</p>
 
 	<li>If the structure is already shown, then you will be prompted
 	to associate the sequence with an existing view of the selected
-	structure.</li>
+	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>
-		Additionally, if several of the sequences in the currently selected
-		region of the alignment have associated structures, then Jalview will
-		provide a 'View <em>X</em> structures' entry in the submenu. This
-		option will open a new Jmol view containing 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>)
+		<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
 Sequence", and one of the submenus:</p>
@@ -69,9 +70,8 @@ Sequence", and one of the submenus:</p>
 	EBI, to fetch the PDB file with the entered Id.<br>
 	</li>
 
-	<li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the
-	EBI, to discover PDB ids for all the sequences in the alignment which
-	have valid Uniprot names / accession ids.</li>
+	<li>Discover PDB Ids - Jalview uses the sequence's ID to query WSDBFetch, provided by the
+	EBI, and any enabled DAS servers, to discover PDB ids associated with the sequence.</li>
 </ul>
 
 <p><strong>Importing PDB Entries or files in PDB format</strong><br>
