JAL-4090 JAL-4147 documentation for revised sequence associated annotation display...

[jalview.git] / help / help / html / features / xsspannotation.html

diff --git a/help/help/html/features/xsspannotation.html b/help/help/html/features/xsspannotation.html
index 870b005..5f33dfe 100644 (file)
--- a/help/help/html/features/xsspannotation.html
+++ b/help/help/html/features/xsspannotation.html
@@ -29,8 +29,9 @@
   <p>
     Jalview can process PDB data associated with sequences to display
     values extracted from the <em>Temperature Factor</em> column for
-    corresponding sites, and secondary structure from DSSP or RNAView
-    (as appropriate).
+    corresponding sites, and secondary structure from DSSP. For computationally determined structures, jalview will show
+    model quality data encoded in the temperature factor column as <em>AlphaFold Reliability</em> (PLDDT) or <em>Model
+      Quality</em> as appropriate.
   </p>
   <p>
     <strong>Extracting data from PDB files<br /></strong>Annotation is
@@ -43,20 +44,21 @@
     the <strong>Add Reference Annotation</strong> in the <strong>Selection</strong>
     and <strong>Sequence ID</strong> sub-menus of the Sequence ID
     Panel's popup menu.<br /> <em>Please note:</em>Protein structures
-    are analysed <em>in situ</em>, but Jalview employs a web service to
-    process RNA structures which can cause long delays if your internet
-    connection is slow.
+    are analysed <em>in situ</em>. 
   </p>
   <p>
     The <a href="../menus/alwannotation.html"><em>Annotations</em>
       alignment menu</a> provides settings useful for controlling the
-    display of secondary structure annotation.
-  </p>
+    display of sequence-associated annotation. To compare several tracks from different structures for one or more
+    sequences, use 'sort by label' - which will also display PDB and Chain IDs for secondary structure and temperature
+    factor/quality annotation tracks for easier identification.
+    </p>
   <p>
     <strong>Shading sequences by associated structure
       annotation<br />
     </strong>The annotation colouring dialog (opened by the <strong>Colour&rarr;By
-      Annotation</strong> option) allows sequences with associated secondary
+      Annotation</strong> option) or by right-clicking a particular annotation tracks's label allows sequences with
+    associated secondary
     structure data to be shaded according to secondary structure type.
     Once the dialog is opened, select the <em>Per Sequence</em> option
     and then choose <em>Secondary structure</em> from the dropdown menu.<br />When