X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=4904856d1fd311df7aa55befe18eeedad3c17fb6;hb=e66bdc1c0086ab56c56979d9dc6635e81503eb84;hp=71c201154d44a1905fa88068e0089e22de2dc991;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 71c2011..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)
- * 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 
@@ -38,14 +38,24 @@ 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>To associate PDB files with a sequence, right click on a sequence
+	<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
 Sequence", and one of the submenus:</p>
 
@@ -60,9 +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>
@@ -75,6 +84,18 @@ Jalview will also read PDB files directly. Simply load in the file as
 you would an alignment file. The sequences of any peptide chains will be
 extracted from the file and viewed in the alignment window.</p>
 
+<p>
+<strong>Associating a large number of PDB files to sequences
+in an alignment</strong><br /> It is often the case when working with
+structure alignments that you will have a directory of PDB files, and
+an alignment involving one or more of the structures. If you drag a
+number of PDB files onto an alignment in the Jalview desktop, Jalview
+will give you the option of associating PDB files with sequences that
+have the same filename. This means, for example, you can automatically
+associate PDB files with names like '1gaq.pdb' with sequences that
+have an ID like '1gaq'.
+<br/><em>Note: This feature was added in Jalview 2.7</em>
+</p>
 <p><em>Note for jalview applet users:<br>
 Due to the applet security constraints, PDB Files can currently only be
 imported by cut and paste of the PDB file text into the text box opened
@@ -90,11 +111,11 @@ Features"</strong> menu item and the <a href="featuresettings.html">Feature
 Settings dialog box</a>.</p>
 
 <p><em><strong>Outstanding problem with cut'n'pasted
-files in Jalview 2.6</strong><br>
+files in Jalview 2.6 and Jalview 2.7</strong><br>
 Structures imported via the cut'n'paste dialog box will not be correctly
 highlighted or coloured when they are displayed in structure views,
 especially if they contain more than one PDB structure. See the bug
-report at http://issues.jalview.org/JAL-623 for news on this problem.</em></p>
+report at http://issues.jalview.org/browse/JAL-623 for news on this problem.</em></p>
 </body>
 </html>
 
