JAL-4019 Clarification of position on 'X' in help text

diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html
index 3b16d41..9ba0578 100755 (executable)
--- a/help/help/html/colourSchemes/index.html
+++ b/help/help/html/colourSchemes/index.html
@@ -459,7 +459,7 @@ td {
                                                        <td>I</td>
                                                        <!--Inosine-->
                                                        <td>X</td>
-                                                       <!--Xanthine (sometimes Unknown)-->
+                                                       <!--Unknown (sometimes Xanthine)-->
                                                        <td>R</td>
                                                        <!--Unknown Purine-->
                                                        <td>Y</td>

diff --git a/help/help/html/colourSchemes/nucleotideambiguity.html b/help/help/html/colourSchemes/nucleotideambiguity.html
index bf097cd..c1ab548 100755 (executable)
--- a/help/help/html/colourSchemes/nucleotideambiguity.html
+++ b/help/help/html/colourSchemes/nucleotideambiguity.html
@@ -39,6 +39,9 @@ td {
   <p>
   This colour scheme was devised by Suzanne Duce and the Jalview Team to highlight ambiguity codes used in nucleotide sequences.
   </p>  
+  <p>
+  The use of X to represent an unknown base is acknowledged, but this is not recommended as the symbol refers to xanthine (see IUPAC-IUB Commission on Biochemical Nomenclature (CBN). <a href="https://iupac.qmul.ac.uk/misc/naabb.html">Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents.</a>)
+  </p>
   <div align="center">
     <table width="200" border="1">
       <tr>
@@ -67,7 +70,7 @@ td {
       </tr>
       <tr>
         <td bgcolor="#4f6f6f">X</td>
-        <td>Xanthine (sometimes Unknown)</td>
+        <td>Unknown (sometimes Xanthine)</td>
       </tr>
       <tr>
         <td bgcolor="#CD5C5C">R</td>