JAL-1957 JAL-1479 updated SIFTS user docs

diff --git a/help/html/features/sifts_mapping_output.png b/help/html/features/sifts_mapping_output.png
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diff --git a/help/html/features/siftsmapping.html b/help/html/features/siftsmapping.html
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--- a/help/html/features/siftsmapping.html
+++ b/help/html/features/siftsmapping.html
@@ -9,8 +9,8 @@
   <p><strong>SIFTS Mapping</strong></p>
   
   <p>
-       SIFTS (Structure integration with function, taxonomy
-       and sequences) provides an up-to-date resource for residue-level
+       SIFTS (Structure Integration with Function, Taxonomy
+       and Sequences) provides an up-to-date resource for residue-level
        mapping between Uniprot and PDB entries. The information is updated and
        released weekly simultaneously with the release of new PDB entries.
        SIFTS Entries are published as XML files and made publicly available via an FTP
@@ -18,7 +18,8 @@
   </p>
        
   <p>
-    At the point of viewing a PDB structure, Jalview downloads a SIFTS file 
+    At the point of viewing a PDB structure, if the default mapping method is set as 'SIFTS', 
+    Jalview will download a SIFTS file 
        for the target entry and uses it to accurately map the sequence residues with the 
        structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch 
        Alignment algorithm to  map sequence residues to structure residues, and that may not 
@@ -26,18 +27,38 @@
   </p>
   
   <p>
-       The default method for 'Sequence &harr; Structure' mapping can be configured 
-       in the Structure tab in the <strong>Tools &rarr; Preferences</strong> dialog box. When 'SIFTS' 
-       is enabled as the default, all mappings between 'Sequence &harr; Structure' is 
-       performed via SIFTS provided that there is a valid SIFTS entry for PDB structure. If no 
-       valid SIFTS resource is available, then the 'Sequence &harr; Structure' mapping falls 
-       back to Needleman and Wunsch Alignment algorithm.
+  <strong>Configuration</strong><br/>
+       The default mapping method can be configured via <strong>Tools &rarr; Preferences &rarr; 
+       Structure tab</strong> Then scroll to the 'Sequence &harr; Structure method' section of 
+       the dialog box and change the default method. When 'SIFTS' is enabled as the default, all 
+       mappings between 'Sequence &harr; Structure' is performed via SIFTS provided that there 
+       is a valid SIFTS resource for the PDB entry. If no valid SIFTS resource is available, then 
+       the 'Sequence &harr; Structure' mapping falls back to Needleman and Wunsch Alignment algorithm.
   </p>
        
-  <p>To verify the mapping method used, you can view the mapping output via the structure viewer menu <strong>File &rarr; View mapping.</strong> A sample mapping output can be seen in the screenshot below. The highlighted position shows the method used. </p>     
+  <p><strong>Multi-Chain Mappings</strong>
+  <br/>One of the main merits of SIFTS is the ability to accurately achieve multi-chain mapping 
+  (one-to-many) between a single Uniprot sequence and its corresponding multiple chains in 
+  PDB. Consequently, mousing over the uniprot sequence in the alignment window results 
+  to highlighting multiple corresponding positions in the structure viewer for the mapped chains. 
+  </p>
   <p>
-       <img src="sifts_mapping_output.png" align="left" alt="SIFTS mapping output" />
+  To see this in action, load uniprot sequence for FER1_MAIZE then veiw PDB structure for 3B2F, you
+  will notice that mousing over the sequence results to two positions being highlighted in the 
+  structure, also colouring the sequence transfers the color to all the mapped chains in the structure.
   </p>
+  
+  <p>
+  <Strong>Viewing Mapping Output</Strong> <br/>
+  The mapping output is accessible via <strong>File &rarr; View mapping</strong> menu of the structure 
+  viewers. The screenshot below is the mapping output for the <Strong>{FER1_MAIZE &harr; 3B2F}</Strong> 
+  example described above. Observe that all the two chains were mapped. The mapping method used can be 
+  seen within the area highlighted with red boarder. This is useful for visually ascertaining the 
+  mapping method when in doubt.    
+  <p>
+       
+       &emsp;<img src="sifts_mapping_output.png" align="left" alt="SIFTS mapping output" />
+ 
        
   <p><em>SIFTS Mapping integration was added in Jalview 2.9.1</em></p>