From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 18 Nov 2014 11:32:25 +0000 (+0000)
Subject: Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git... 
X-Git-Tag: Release_2_8_2b1^2~26
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3855e31972baa9f344f97b7dda185b73e1c320b8;p=jalview.git

Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
---

3855e31972baa9f344f97b7dda185b73e1c320b8
diff --cc help/html/features/preferences.html
index 0744c51,5d4ab4d..657359e
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@@ -113,17 -113,15 +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. Enter the full path to the Chimera executable program.  
 +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>