Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 21caca1..f60da1a 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -53,11 +53,12 @@
       '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.
@@ -68,9 +69,14 @@
         <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
@@ -84,10 +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>
@@ -96,9 +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