JAL-2189 format help

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

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index e62b2a7..21caca1 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -46,8 +46,8 @@
       </ul>
     </li>
     <li><strong>Selecting Structures</strong><br />You can select
-      the structures to 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
@@ -59,9 +59,16 @@
             Entries</strong> option from the drop down menu at the top of the
           dialog box.</li>
       </ul></li>
-    <li>To view selected structures, click the <strong>"View"</strong>
-      button.
-    </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>
+      </ul></li>
   </ol>
 
   The
@@ -112,13 +119,12 @@
     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 />
-  </p>
-  <p>
-    <strong>Retrieving sequences from the PDB</strong><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>
@@ -151,7 +157,7 @@
       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
@@ -161,7 +167,7 @@
     wwwPDB. If you prefer (for any reason) to download data as PDB files
     instead, then first close Jalview, and add the following line to
     your .jalview_properties file:<br />
-    <code> DEFAULT_STRUCTURE_FORMAT=PDB </code>
+    <code> PDB_DOWNLOAD_FORMAT=PDB </code>
     <br /> When this setting is configured, Jalview will only request
     PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
       file support was added in Jalview 2.10.</em>