Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[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 58b06db..0ae0684 100755 (executable)
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -64,6 +64,9 @@
     <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong>
         Preferences</a> tab contains settings affecting behaviour when editing alignments.
     </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>
@@ -222,17 +225,15 @@
     <em>Add Temperature Factor annotation to alignment</em> - if
     selected, values extracted from the Temperature Factor column for
     the backbone atoms in the PDB file will be extracted as annotation
-    lines shown on the alignment.
+    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 or CHIMERA for
+    <em>Default structure viewer</em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
     viewing 3D structures.
   <p>
-    <em>Path to Chimera program</em> - Optional, as Jalview will search
-    standard installation paths for Windows, Linux or MacOS. If you have
-    installed Chimera in a non-standard location, you can specify it
-    here, by entering the full path to the Chimera executable program.
-    Double-click this field to open a file chooser dialog.
-  <p>
+    <em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
+    standard installation paths for Windows, Linux or MacOS. If Jalview cannot locate the installation for your selected structure viewer, a dialog will be shown. If you have
+    installed the chosen viewer in a non-standard location, you can specify it
+    here, by entering the full path to its executable.<br/>For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also <em>double-click this field</em> to open a file chooser dialog.</p>
   <p>
     <em>PDB Fields shown in Search and Structure Summaries</em> - ticks
     in this table indicate fields shown by default when browsing results
@@ -420,6 +421,14 @@
     <em>Sort with New Tree</em> - When selected, any trees calculated or
     loaded onto the alignment will automatically sort the alignment.
   </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