X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=04612094d9637878f8a9bd9dacafd3e5274968d1;hb=3ab582bfeeab1563bedf60e97994e63e672d2e31;hp=d9582ec72f042f415283ee7d6c2da0b05e636165;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html
index d9582ec..0461209 100644
--- a/help/html/features/structurechooser.html
+++ b/help/html/features/structurechooser.html
@@ -31,7 +31,7 @@
   <p>
     The Structure Chooser interface allows you to interactively select
     which PDB structures to view for the currently selected set of
-    sequences. It's opened by selecting the <strong>"3D
+    sequences. It is opened by selecting the <strong>"3D
       Structure Data.."</strong> option from the Sequence ID panel's <a
       href="../menus/popupMenu.html">pop-up menu</a>. The dialog
     provides:
@@ -46,33 +46,47 @@
     <li>Association of structure data from a local file (in mmCIF
       or PDB format)</li>
   </ul>
-
+  <p>
+    <strong>Selecting and Viewing Structures</strong>
+  </p>
+  <p>
+    Once one or more structures have been selected, pressing the <strong>View</strong>
+    button will import them into <a
+      href="viewingpdbs.html#afterviewbutton">a new or existing
+      structure view</a>.
+  </p>
   <p>
     <strong>Automated discovery of structure data</strong>
   </p>
-  <p>After selecting "3D Structure Data ..", Jalview queries the PDB
-    via the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB ids
+  <p>
+    After selecting "3D Structure Data ..", Jalview queries the PDB via
+    the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB IDs
     associated with the sequence. It does this based on the sequence's
-    ID string, and any other associated database IDs.</p>
+    ID string, and any other associated database IDs. <br />
+    <br />
   <p>
-    <strong>Exploration of meta-data for available structures</strong>
+    <strong><a name="cachedstructview">Viewing existing
+        structures for your sequences</a></strong>
+  </p>
+  <p>
+    If you have already loaded 3D structure data for the selected
+    sequences, the structure chooser will first open with the <strong>Cached
+      Structures View</strong>. This view shows associations between each
+    sequence, and chains for 3D structure files already in memory. If
+    you want to download additional structures, select one of the other
+    options from the drop down menu.
   </p>
-  <p>Information on each structure available is displayed in columns
-    in the dialog box. By default, only the title, resolution and PDB
-    identifier are shown, but many more are provided by the PDBe. To
-    configure which ones are displayed, select the 'Configure Displayed
-    Columns' tab and tick the columns which you want to see.</p>
   <p>
     <strong>Selection of the best structure for each sequence</strong>
   </p>
   <p>Jalview can automatically select the best structures according
-    to meta-data provided by the PDB. By default, the 'Best Quality'
-    structure for each sequence will be selected, but clicking on the
-    drop down menu allows other criteria to be chosen, including
-    Resolution (only defined for X-Ray structures), Highest Protein
-    Chain etc. When 'Invert' is selected, structures are selected in
-    reverse order for the current criteria (e.g. worst quality rather
-    than best).</p>
+    to meta-data provided by the PDB. For alignments with no existing
+    structure data, the 'Best Quality' structure for each sequence will
+    by default be selected, but clicking on the drop down menu allows
+    other criteria to be chosen, including Resolution (only defined for
+    X-Ray structures), Highest Protein Chain etc. When 'Invert' is
+    selected, structures are selected in reverse order for the current
+    criteria (e.g. worst quality rather than best).</p>
   <p>
 
     <img src="schooser_main.png" style="width: 464px; height: 369px;">
@@ -83,13 +97,20 @@
 	<p><img src="schooser_cached.png"> -->
     <br>The screenshot above shows the Structure Chooser interface
     along with the meta-data of auto-discovered structures for the
-    sample alignment. Note however that if no structures were
-    auto-discovered, a different interface for manual association will
-    be invoked as seen in the screenshot below.
+    sample alignment. If no structures were
+    auto-discovered, options for manually associating PDB records will be shown (see below).
+  <p>
+    <strong>Exploration of meta-data for available structures</strong>
+  </p>
+  <p>Information on each structure available is displayed in columns
+    in the dialog box. By default, only the title, resolution and PDB
+    identifier are shown, but many more are provided by the PDBe. To
+    configure which ones are displayed, select the 'Configure Displayed
+    Columns' tab and tick the columns which you want to see.</p>
   <p>
     <img src="schooser_enter-id.png"
       style="width: 464px; height: 369px;">
-  <p>
+      <br/>
     <strong>Manual selection/association of PDB files with
       Sequences</strong>
   </p>
@@ -104,14 +125,6 @@
       for your sequence. The PDB Rest API, provided by EMBL-EBI, is used
       to validate and fetch structure data.<br></li>
   </ul>
-  <p>
-    <strong>Viewing existing structures for your sequences</strong>
-  </p>
-  <p>
-    If you have previously associated structure data on the alignment,
-    selecting <strong>Cached PDB Entries</strong> from the drop down
-    menu allows you to select these structures for display.
-  </p>
 
   <p>
     <em>The Structure Chooser interface was introduced in Jalview