X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=b3d44dbf1c49e3c5623d1b4b5fc0f309ed568396;hb=d30a1e3993c5538efdecd3149dc8e5a1e4e42936;hp=eab7cfc2cc7b8739a0e3b8523cc63ae80f55a553;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html
index eab7cfc..b3d44db 100755
--- a/help/html/colourSchemes/clustal.html
+++ b/help/html/colourSchemes/clustal.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
  * 
@@ -40,9 +40,10 @@ td {
     is assigned a colour if the amino acid profile of the alignment at
     that position meets some minimum criteria specific for the residue
     type.</p>
-  <p>The table below gives these criteria as clauses: {+X%,xx,y},
-    where X is the minimum percentage presence for any of the xx (or y)
-    residue types.</p>
+  <p>The table below gives these criteria as clauses: {&gt;X%,xx,y},
+    where X is the threshold percentage presence for any of the xx (or y)
+    residue types.
+    <br>For example, K or R is coloured red if the column includes more than 60% K or R (combined), or more than 80% of either K or R or Q (individually).</p>
   <div align="center">
     <p>&nbsp;</p>
     <table border="1">
@@ -52,70 +53,81 @@ td {
       <tr>
         <td><table border="1">
             <tr>
+              <th>Category</th>
+              <th>Colour</th>
               <th>Residue at position</th>
-              <th>Applied Colour</th>
-              <th>{ Threshhold, Residue group }</th>
+              <th>{ Threshold, Residue group }</th>
             </tr>
             <tr>
+              <td rowspan="2">Hydrophobic</td>
+              <td rowspan="2" bgcolor="#80a0f0">BLUE</td>
               <td>A,I,L,M,F,W,V</td>
-              <td bgcolor="#80a0f0">BLUE</td>
-              <td>{+60%, WLVIMAFCHP}</td>
+              <td>{&gt;60%, WLVIMAFCHP}</td>
             </tr>
             <tr>
-              <td>R,K</td>
+              <td>C</td>
+              <td>{&gt;60%, WLVIMAFCHP}</td>
+            </tr>
+            <tr>
+              <td>Positive charge</td>
               <td bgcolor="#f01505">RED</td>
-              <td>{+60%,KR},{+80%, K,R,Q}</td>
+              <td>K,R</td>
+              <td>{&gt;60%,KR},{&gt;80%, K,R,Q}</td>
             </tr>
             <tr>
-              <td>N</td>
-              <td bgcolor="#15c015">GREEN</td>
-              <td>{+50%, N}, {+85%, N,Y}</td>
+              <td rowspan="2">Negative charge</td>
+              <td rowspan="2" bgcolor="#c048c0">MAGENTA</td>
+              <td>E</td>
+              <td>{&gt;60%,KR},{&gt;50%,QE},{&gt;85%,E,Q,D}</td>
             </tr>
             <tr>
-              <td>C</td>
-              <td bgcolor="#80a0f0">BLUE</td>
-              <td>{+60%, WLVIMAFCHP}</td>
+              <td>D</td>
+              <td>{&gt;60%,KR}, {&gt;85%, K,R,Q}, {&gt;50%,ED}</td>
             </tr>
             <tr>
-              <td>C</td>
-              <td bgcolor="#f08080">PINK</td>
-              <td>{100%, C}</td>
+              <td rowspan="3">Polar</td>
+              <td rowspan="3" bgcolor="#15c015">GREEN</td>
+              <td>N</td>
+              <td>{&gt;50%, N}, {&gt;85%, N,Y}</td>
             </tr>
             <tr>
               <td>Q</td>
-              <td bgcolor="#15c015">GREEN</td>
-              <td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td>
+              <td>{&gt;60%,KR},{&gt;50%,QE},{&gt;85%,Q,E,K,R}</td>
             </tr>
             <tr>
-              <td>E</td>
-              <td bgcolor="#c048c0">MAGENTA</td>
-              <td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td>
+              <td>S,T</td>
+              <td>{&gt;60%, WLVIMAFCHP}, {&gt;50%, TS}, {&gt;85%,S,T}</td>
             </tr>
             <tr>
-              <td>D</td>
-              <td bgcolor="#c048c0">MAGENTA</td>
-              <td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td>
+              <td>Cysteines</td>
+              <td bgcolor="#f08080">PINK</td>
+              <td>C</td>
+              <td>{>85%, C}</td>
             </tr>
             <tr>
-              <td>G</td>
+              <td>Glycines</td>
               <td bgcolor="#f09048">ORANGE</td>
-              <td>{+0%, G}</td>
+              <td>G</td>
+              <td>{&gt;0%, G}</td>
             </tr>
             <tr>
-              <td>H,Y</td>
-              <td bgcolor="#15a4a4">CYAN</td>
-              <td>{+60%, WLVIMAFCHP}, {+85%,
-                W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
+              <td>Prolines</td>
+              <td bgcolor="#c0c000">YELLOW</td>
+              <td>P</td>
+              <td>{&gt;0%, P}</td>
             </tr>
             <tr>
-              <td>P</td>
-              <td bgcolor="#c0c000">YELLOW</td>
-              <td>{+0%, P}</td>
+              <td>Aromatic</td>
+              <td bgcolor="#15a4a4">CYAN</td>
+              <td>H,Y</td>
+              <td>{&gt;60%, WLVIMAFCHP}, {&gt;85%,
+                W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
             </tr>
             <tr>
-              <td>S,T</td>
-              <td bgcolor="#15c015">GREEN</td>
-              <td>{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}</td>
+              <td>Unconserved</td>
+              <td>WHITE</td>
+              <td>any / gap</td>
+              <td>If none of the above criteria are met</td>
             </tr>
           </table></td>
       </tr>
