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

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

diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md
index f3888cf..969c53f 100644 (file)
--- a/help/markdown/releases/release-2_11_3_0.md
+++ b/help/markdown/releases/release-2_11_3_0.md
@@ -21,7 +21,7 @@ channel: "release"
 - <!-- JAL-4274 --> Command line options and configurable bitmap export preferences for height, width and scale factor
 - <!-- JAL-4307 --> Show or hide ligands in a Jmol structure view via View Ligands submenu
 
-### Improved support for working with computationally determined models
+### Improved support for working with structures and computationally determined models
 - <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
 - <!-- JAL-4095 --> Interactive picking of low pAE score regions
 - <!-- JAL-4027 --> contact matrix datatype in Jalview
@@ -35,6 +35,8 @@ channel: "release"
 - <!-- JAL-4124 --> Store/Restore PAE data and visualisation settings from Jalview Project
 - <!-- JAL-4281 --> Store and restore adjustable ID margin and annotation panel height in Jalview projects
 - <!-- JAL-4083 --> Multiple residue sidechain highlighting in structure viewers from PAE mouseovers
+- <!-- JAL-4147 --> Per-structure and chain shown when annotation shown sorted by label enabling secondary structure and temperature factor scores from different chains and structures for the same sequence to be visually compared.
+
 
 ### Jalview on the command line
 - <!-- JAL-4160,JAL-629,JAL-4262,JAL-4265, --> New command line argument framework allowing flexible batch processing, import of structures, pae matrices and other sequence associated data, and alignment and structure figure generation.