X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=928ea2c4a75b604983010ea5fdc52182fa172d9e;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=1831c3eb11a316c0b2b7bf7433bffc1943781982;hpb=3e0101470a0b6d41eac74c129f963a6ed0e69e2f;p=jalview.git

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 1831c3e..928ea2c 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -113,14 +113,16 @@ will be loaded.</p>
 <p><a name="structure"><strong>&quot;Structure&quot;
 Preferences tab</strong></a><em> added in Jalview 2.8.2</em></p>
 <p><em>Process secondary structure from PDB</em> - if selected, then structure information
-read from PDB will be processed to derive secondary structure annotation.
-<p><em>Use RNAView for secondary structure</em> - if selected, the RNAView service will be 
-automatically called to derive secondary structure information.
-<p><em>Add secondary structure annotation to alignment</em> - if selected, PDB secondary structure
-annotation will be shown on the alignment when available.
-<p><em>Add Temperature Factor annotation to alignment</em> - if selected, PDB Temperature Factor
-annotation will be shown on the alignment when available. 
+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 chains in the structure.
+<p><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. 
 <p><em>Default structure viewer</em> - choose JMOL or CHIMERA 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><a name="connections"><strong>&quot;Connections&quot;
 Preferences tab</strong></a></p>
