From: jprocter <Jim Procter>
Date: Mon, 25 Apr 2011 12:57:43 +0000 (+0000)
Subject: documentation for JAL-824 and JAL-621
X-Git-Tag: Release_2_7~202
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6b1e88e1329c93de084fec9b2db0bda458ab6740;p=jalview.git

documentation for JAL-824 and JAL-621
---

diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html
index 6aa2eaf..d23e1d6 100644
--- a/help/html/features/jmol.html
+++ b/help/html/features/jmol.html
@@ -134,15 +134,21 @@ be measured from it to any other atom in the structure.</p>
 	<ul>
 		<li><strong>Show Chains<br>
 		</strong><em>Select which of the PDB file's chains are to be displayed.</em></li>
-	</ul>
+		<li><strong>Colour by ..<br></strong><em>Submenu allowing specific alignment views to be selected for colouring associated chains in the structure display. This menu contains all the alignment views associated with the structure view, with those used to colour the view indicated by ticks. Addditionally, it contains the following menu entries:</em>
+		<ul><li><strong>Select many views<br></strong><em>When this option is enabled, selecting an alignment view adds it to the set used to colour the structures. Use this when colouring structures related to a number of alignments involving different domains or chains which are shown in the same structure view.</em>
+		</li>
+    <li><strong>Select all views<br></strong><em>This is only enabled when </em><strong>Select many views</strong><em> is also enabled, and will add all associated views to the set used to colour the structure display.</em>
+  </li>
+    <li><strong>Invert selection<br></strong><em>This is only enabled when </em><strong>Select many views</strong><em> is also enabled, and will replace the current set of views with any remaining views not currently used to colour the structure display.</em>
+  </li></ul></li>
 	<li><strong>Colours<br>
 	</strong>
 	<ul>
 		<li><strong>By Sequence<br>
 		</strong><em> Colours each residue in the structure with the colour of its
 		corresponding residue in the associated sequence as rendered in the
-		associated alignment view, including any Uniprot sequence features or
-		region colourings.<br>
+		associated alignment views, including any Uniprot sequence features or
+		region colourings.<br/>Pick which of the associated alignment views are used to colour the structures using the <strong>View&#8594;Colour by ..</strong> sub menu.</em><br>
 		Residues which only exist in the PDB structure are coloured white if
 		they are insertions (relative to the associated sequence in the
 		alignment) and grey if they are N or C terminal flanks outside the
@@ -153,6 +159,7 @@ be measured from it to any other atom in the structure.</p>
 		</strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
 		Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
 		residues in blue.</em></li>
+		<li><strong>Colour with Jmol<br></strong><em>Defers any colouring operations to Jmol. Select this if you want to use the Jmol scripting interface or menu to modify the view directly.</em></li>
 		<li><strong>Standard and User Defined Jalview
 		colourschemes.<br>
 		</strong><em>The remaining entries apply the colourschemes available from