X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=b1ad4bae86c77cc534a3285c370a2a3e864cb54e;hb=bcd5c6cc4f8e2ad6a510f701d1caefe59b6a88f0;hp=edb3762903b50c3ea5dd924d08e1a93bbc05946c;hpb=4687a9d3adb02abca831fbb119a54153bc2a19ca;p=jalview.git

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index edb3762..b1ad4ba 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -46,64 +46,74 @@
       </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 Structures</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 />
+      <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>
-    <li>To view selected structures, click the <strong>"View"</strong>
-      button.
-    </li>
   </ol>
-
-  The
-  <a href="jmol.html">Jmol viewer</a> has been included since Jalview
-  2.3. Jalview 2.8.2 included support for
-  <a href="chimera.html">Chimera</a>, 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>
+    <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 <a href="chimera.html">Chimera</a>,
+    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
     the <a href="xsspannotation.html">Annotation from Structure</a> page
     for more information.
   </p>
+  <p>
+    <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 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">align this structure</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
@@ -112,12 +122,12 @@
     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>
@@ -150,7 +160,7 @@
       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