JAL-1957 JAL-1479 tweak SIFTS mappings documentation, add to what’s new section

diff --git a/help/help.jhm b/help/help.jhm
index 1760d43..7e14204 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -141,6 +141,7 @@
    
    <mapID target="biojson" url="html/features/bioJsonFormat.html" />
    <mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
+   <mapID target="siftsmapping" url="html/features/siftsmapping.html" />
    <mapID target="pdbchooser" url="html/features/structurechooser.html" />
    <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
    <mapID target="biojsmsa" url="html/features/biojsmsa.html" />

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index ed95a61..bf1710c 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -25,7 +25,7 @@
                        <tocitem text="What's new" target="new" expand="true">
                                <tocitem text="Retrieval from ENSEMBL" target="ensemblfetch" />
                                <tocitem text="UniProt Free Text Search" target="uniprotfetcher" />
-                               
+                               <tocitem text="SIFTS for mapping PDB structures to UniProt" target="siftsmapping" />
                                <tocitem text="Latest Release Notes" target="release"/>
                </tocitem>
                

diff --git a/help/html/features/siftsmapping.html b/help/html/features/siftsmapping.html
index 80c0294..9492d70 100644 (file)
--- a/help/html/features/siftsmapping.html
+++ b/help/html/features/siftsmapping.html
@@ -21,11 +21,10 @@
     record and use that information to construct a mapping between the
     sequence and downloaded structure.</p>
   <p>If, for some reason, no SIFTS mapping data exists, then Jalview
-    will generate a mapping using its built-in Needleman and Wunsch
-    global alignment algorithm. This method of mapping was used for all
-    structures prior to version 2.10.
-  <p>
-    <strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
+    will generate a mapping using the built-in Needleman and Wunsch
+    global alignment algorithm. This is how sequence-structure mappings
+    were created before version 2.10.</p>
+  <p><strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
     Configuration options controlling whether SIFTS mappings are used
     can be found in the <strong>Tools &rarr; Preferences &rarr;
       Structure tab</strong>, under 'Sequence &harr; Structure method'.<br /> <em>Note:</em>
@@ -38,30 +37,29 @@
     <strong>Multi-Chain Mappings</strong> <br />SIFTS gives Jalview the
     ability to display multi-chain mappings between UniProt sequences
     and PDB structure data. This is important when working with
-    multimeric proteins, since the biological unit will contain several
+    multimeric proteins, when the biological assembly can contain several
     structures for the same protein sequence. Multi-chain mapping allows
     all residues in a structure to be located in the alignment, and
     also, when shading the structure by sequence colours, enables
     conservation patterns between oligomer interfaces to be explored.
   </p>
-  <p>To see this in action, load uniprot sequence for FER1_MAIZE
-    then veiw PDB structure for 3B2F, you will notice that mousing over
+  <p>To see this in action, Retrieve the UniProt sequence
+    FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over
     the sequence results to two positions being highlighted in the
-    structure, also colouring the sequence transfers the color to all
+    structure, and colouring the alignment transfers the color to all
     the mapped chains in the structure.</p>
 
   <p>
     <Strong>Viewing Mapping Output</Strong> <br /> The mapping provided
     by the SIFTS record 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, and confirms that all two chains
-    were mapped. The mapping method used can be seen within the area
-    highlighted with red boarder.
+    shows the mapping created between UniProt sequence FER1_MAIZE and proteins in PDB 3B2F, which reports thattwo chains
+    were mapped. The mapping method is also reported (highlighted with red border).
   <p>
 
     &emsp;<img src="sifts_mapping_output.png" align="left"
       alt="SIFTS mapping output" />
+      <br/>
   <p>
     <em>SIFTS Mapping integration was added in Jalview 2.10</em>
   </p>

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index ac48313..1d2367d 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -52,8 +52,9 @@
       <ul>
         <li><strong>More accurate structure mappings.</strong>
           Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
-          to match structures to UniProt sequences, even for structures
-          containing multiple copies of a sequence.</li>
+          to <a href="features/siftsmapping.html">match structures
+            to UniProt sequences</a>, even for structures containing
+          multiple copies of a sequence.</li>
         <li><strong>Import structures as mmCIF</strong>. Jalview
           now downloads data from the EMBL-EBI's PDBe site as mmCIF.
           mmCIF files allow Jalview to handle very large structures,