X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=506beef6e1f5df2316f89952f9d69e94c8abc46b;hb=c248aad32a357e7440b2e5ab3ea8c5fddbb26b84;hp=bece211d0a597f726b54cae24ae319d7412aebb0;hpb=dbb8e925003ee2249a65bed6e6c74b378b673a18;p=jalview.git

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index bece211..506beef 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -29,18 +29,17 @@
 	Jalview can be used to view protein structures by following the steps below:
 	<ol>
 		<li>Select the <strong>"View Structure"</strong> option from a
-			sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.
+			sequence's <a href="../menus/popupMenu.html">pop-up menu</a> to invoke the <a href="structurechooser.html">Structure Chooser</a> interface.
 			<ul>
-				<li>If one or more structures exists for the given sequence, the <strong>'Structure Chooser'</strong>
+				<li>If one or more structures exists for the given sequence, the <a href="structurechooser.html">Structure Chooser</a>
 					dialogue is opened with a list of the found structures meta-data.</li>
-				<li>However, if no structure was found, the <strong>'Structure Chooser'</strong> dialogue is opened with options for manual association of PDB structures.</li>
+				<li>However, if no structure was found, the <a href="structurechooser.html">Structure Chooser</a> interface is opened with options for manual association of PDB structures.</li>
 			</ul> 
 			</li>
-		<li>Choose the structure to view from the presented structures
-			summary list. This can be done either manually by clicking directly
-			on the desired structure from the list, or automatically by
-			using the filter combo-box which enables filtering on certain
-			criteria like quality, resolution, etc. The best structure for the chosen criteria is automatically selected by the filtration process. </li>
+		<li>Choose the structure to view from the discovered list. This can be done either manually by clicking directly
+			on the desired structure(s) in the list, or automatically by
+			using the drop-down menu on the interface to filter and auto-select the best structure based on certain
+			criteria like quality, resolution, etc.</li>
 		<li>When the desired structure(s) have been selected, they can be
 			viewed by clicking the <strong>"View"</strong> button below the summary list.
 		</li> 
@@ -101,27 +100,7 @@ structure is selected, one of the following will happen:</p>
 	<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><strong>Associating PDB files with Sequences</strong></p>
-	<p>Since Jalview 2.8.3, discovery of PDB Id associated to a sequence happens automatically when the <strong>"View Structure"</strong> option is selected
-	from a sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Jalview uses the sequence's ID to query the PDB Rest API, provided by the
-	EBI to discover PDB ids associated with the sequence. </p>
-	
-	<p><strong>Manual association of PDB files with Sequences</strong> </p>
-	<p>To manually associate PDB files with a sequence, right click on a sequence
-ID and select  the <strong>"View Structure"</strong> option, this opens the <strong>'Structure Chooser'</strong> dialogue. Then pick any of the follwing options listed below from the drop-down menu in the <strong>'Structure Chooser'</strong> panel to proceed with manual association:
 
-<ul>
-	<li><strong>From File</strong> - You can load a PDB file from the local machine or
-	network and associate it with the selected sequence. PDB files
-	associated in this way will also be saved in the <a
-		href="jalarchive.html">Jalview Archive file</a>.<br>
-	</li>
-	<li><strong>Enter PDB Id</strong> - Jalview will use the PDB Rest API, provided by the
-	EBI, to fetch the PDB file with the entered Id.<br>
-	</li>
-</ul>
-
-<strong>Note:</strong> The drop-down menu in the 'Structure Chooser' panel may contain other options employed for filtering structures when one or more structures are auto-discovered.
 
 <p><strong>Importing PDB Entries or files in PDB format</strong><br>
 You can retrieve sequences from the PDB using the <a