JAL-2944 revised docs and structure chooser screen shots

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

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 45d979f..b1ad4ba 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -82,6 +82,7 @@
     provided it is installed and can be launched by Jalview. The default
     viewer can be configured in the <a href="preferences.html#structure">Structure
       tab</a> in the <strong>Tools&rarr;Preferences</strong> dialog box.
+  
   <p>
     Structure data imported into Jalview can also be processed to
     display secondary structure and temperature factor annotation. See
@@ -89,44 +90,30 @@
     for more information.
   </p>
   <p>
-    <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.
+    <img src="schooser_viewbutton.png"
+      style="width: 465px; height: 81px" /><br/> <strong><a
+      name="afterviewbutton">Controlling where the new structures
+        will be shown</a></strong>
+        <br />The Structure Chooser offers several options
+    for viewing a structure. <br/><strong>New View</strong> will open a new
+    structure viewer for the selected structures, but if there are views
+    already open, you can select which one to use, and press the <strong>Add</strong>
+    button. Jalview can automatically superimpose new structures based
+    on the linked alignments - but if this is not desirable, simple
+    un-tick the <strong>Superpose Structures</strong> checkbox.
+
   </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. A message in the structure viewer's
-    status bar will be shown if not enough aligned columns were
-    available to perform a superposition.</p>
   <p>
-    If a <strong>single</strong> PDB structure is selected, one of the
-    following will happen:
+    <em>Superposing structures</em><br/>Jalview superposes structures using
+    the visible portions of any associated sequence alignments. A
+    message in the structure viewer's status bar will be shown if not
+    enough aligned columns were available to perform a superposition.
   </p>
-
-  <ul>
-    <li>If no structures are open, then an interactive display of
-      the structure will be opened in a new window.</li>
-
-    <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"></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
-      selected 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
-    </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for
-      more information about the display.
-    </li>
-  </ul>
-
+  <p>
+  See the <a href="jmol.html">Jmol
+    </a> and <a href="chimera.html">Chimera</a> help pages for
+      more information about their capabilities.</p>
+  
 
   <p>
     <strong>Retrieving sequences from the PDB</strong><br>You can