JAL-2039 rejig instructions for Structure Chooser and clarify what happens after...

[jalview.git] / help / html / features / viewingpdbs.html

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 9cead2d..f60da1a 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -46,30 +46,37 @@
       </ul>
     </li>
     <li><strong>Selecting Structures</strong><br />You can select
-      the structures that you want to open and view by selecting them with
-      the mouse and keyboard.<br />By default, if structures were
+      the structures that you want to open and view by selecting them
+      with the mouse and keyboard.<br />By default, if structures were
       discovered, then some will already be selected according to the
       criteria shown in the drop-down menu. The default criteria is
       'highest resolution', simply choose another to pick structures in
       a different way.<br />
       <ul>
-        <li><strong>Viewing Cached Structures</strong><br />If you
-          have previously downloaded structures for your sequences, they
-          can be viewed by selecting the <strong>Cached PDB
-            Entries</strong> option from the drop down menu at the top of the
-          dialog box.</li>
+        <li><strong>Viewing Cached Structures</strong><br />If
+          previously downloaded structures are available for your
+          sequences, the structure chooser will automatically offer them
+          via the <strong>Cached PDB Entries</strong> view. If you wish
+          to download new structures, select one of the PDBe selection
+          criteria from the drop-down menu.</li>
       </ul></li>
     <li><strong>To view selected structures, click the <strong>"View"</strong>
-      button.</strong><br />
+        button.
+    </strong><br />
       <ul>
         <li>Additional structure data will be downloaded with the
           EMBL-EBI's dbfetch service</li>
         <li><a href="siftsmapping.html">SIFTS</a> records will also
           be downloaded for mapping UniProt protein sequence data to PDB
           coordinates.</li>
+        <li>A new structure viewer will open, or you will be
+          prompted to add structures to existing viewers (see <a
+          href="#afterviewbutton">below</a> for details).
+        </li>
       </ul></li>
   </ol>
-
+  <p>
+  <strong>Structure Viewers in the Jalview Desktop</strong><br/>
   The
   <a href="jmol.html">Jmol viewer</a> has been included since Jalview
   2.3. Jalview 2.8.2 included support for
@@ -83,10 +90,19 @@
     the <a href="xsspannotation.html">Annotation from Structure</a> page
     for more information.
   </p>
-
   <p>
-    If a <strong>single</strong> PDB structure is selected, one of the
-    following will happen:
+    <strong><a name="afterviewbutton">After pressing the
+        'View' button in the Structure Chooser</a></strong><br /> The behaviour of
+    the 'View' button depends on the number of structures selected, and
+    whether structure views already exist for the selected structures or
+    aligned sequences.
+  </p>
+  <p>
+    If multiple structures are selected, then Jalview will always create
+    a new structure view. The selected structures will be imported into
+    this view, and superposed with the matched positions from the
+    aligned sequences.<br /> If a <strong>single</strong> PDB structure
+    is selected, one of the following will happen:
   </p>
 
   <ul>
@@ -95,9 +111,10 @@
 
     <li>If another structure is already shown for the current
       alignment, then you will be asked if you want to add and <a
-      href="jmol.html#align">align this structure</a> to the structure
-      in the existing view. (<em>new feature in Jalview 2.6</em>).
-    </li>
+      href="jmol.html#align"></a> to
+    the structure in the existing view. (<em>new feature in Jalview
+      2.6</em>).
+  </li>
 
     <li>If the structure is already shown, then you will be
       prompted to associate the sequence with an existing view of the
@@ -118,12 +135,12 @@
     retrieved with this service are derived directly from the PDB 3D
     structure data, which can be viewed in the same way above. Secondary
     structure and temperature factor annotation can also be added. <br />
- 
- <br>Jalview
-    will also read PDB files directly - either in PDB format, or <a
-      href="mmcif.html">mmCIF</a>. Simply load in the file as you would
-    an alignment file. The sequences of any protein or nucleotide chains
-    will be extracted from the file and viewed in the alignment window.
+
+    <br>Jalview will also read PDB files directly - either in PDB
+    format, or <a href="mmcif.html">mmCIF</a>. Simply load in the file
+    as you would an alignment file. The sequences of any protein or
+    nucleotide chains will be extracted from the file and viewed in the
+    alignment window.
   </p>
 
   <p>
@@ -156,7 +173,7 @@
       Features"</strong> menu item and the <a href="featuresettings.html">Feature
       Settings dialog box</a>.
   </p>
-  <br/>
+  <br />
   <hr>
   <p>
     <strong>Switching between mmCIF and PDB format for