Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 25d59bf..509fa35 100755 (executable)
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -68,6 +68,9 @@
         Preferences</a> tab allows you to adjust how much memory is
       allocated to Jalview when it is launched.
     </li>
+    <li>The <a href="#hmmer"><strong>&quot;HMMER&quot;</strong>
+        Preferences</a> tab allows you to configure locally installed HMMER tools.
+    </li>
     <li>The <a href="../webServices/webServicesPrefs.html"><strong>&quot;Web
           Service&quot;</strong> Preferences</a> tab allows you to configure the <a
       href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
@@ -213,11 +216,6 @@
     structure information read from PDB will be processed and annotation
     added to associated sequences.
   <p>
-    <em>Use RNAView for secondary structure</em> - if selected, the
-    pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
-    will be called to derive secondary structure information for RNA
-    chains.
-  <p>
     <em>Add secondary structure annotation to alignment</em> - if
     selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
       implementation DSSP</a> will be used to add annotation to polypeptide
@@ -228,7 +226,7 @@
     the backbone atoms in the PDB file will be extracted as annotation
     lines shown on the alignment.<br/><em>Since 2.11.2, scores from the Temperature Column for structures imported via the 3D-Beacons network may be shown instead as model quality or reliability scores.</em>
   <p>
-    <em>Default structure viewer</em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
+    <em><strong>Default structure viewer</strong></em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
     viewing 3D structures.
   <p>
     <em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
@@ -441,6 +439,15 @@
     stored in your .jalview_properties file.
   </p>
   <p>&nbsp;</p>
+  <p>
+    <a name="hmmer"><strong>&quot;HMMER&quot; Preferences tab</strong></a>
+  </p>
+  <p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),
+  then you should specify on this screen the location of the installation (the path to the folder 
+  containing binary executable programs). Double-click in the input field to open a file browser.</p>
+  <p>When this path is configured, the <a href="../menus/alwhmmer.html">HMMER menu</a> will be
+  enabled in the Alignment window.</p>
+  <p>&nbsp;</p>
   <em>Web Services Preferences</em> - documentation for this tab is
   given in the
   <a href="../webServices/webServicesPrefs.html">Web Services