From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 26 Sep 2023 10:59:56 +0000 (+0100)
Subject: JAL-3858 JAL-4090 pae matrix docs. WIP
X-Git-Tag: Release_2_11_4_0~161
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=985903ad810d9ef6ba0d09ff2b29d24e22c0708d;p=jalview.git

JAL-3858 JAL-4090 pae matrix docs. WIP
---

diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html
index e883bdb..d229251 100644
--- a/help/help/html/features/paematrices.html
+++ b/help/help/html/features/paematrices.html
@@ -29,11 +29,20 @@
 			Jalview</strong>
 	</p>
 
-	<p>Predicted Alignment Error (PAE) matrices are produced by deep-learning
-		based 3D-structure prediction pipelines such as AlphaFold. They reflect how reliably two parts of a model have been positioned in space, by giving for each residue the likely error (in Angstroms) between the modelled position and the pair of residues' real relative position.</p>
-		<p>
-		Jalview visualises PAE matrices as an alignment annotation track, shaded from dark green to white, as used on the EBI-AlphaFold website (see )
-		</p>
+	<p>Predicted Alignment Error (PAE) matrices are produced by
+		deep-learning based 3D-structure prediction pipelines such as
+		AlphaFold. They reflect how reliably two parts of a model have been
+		positioned in space, by giving for each residue the likely error (in
+		&Aring;ngstroms) between that residue and every other modelled
+		position the pair of residues' real relative position, if the model
+		and real 3D structure were superimposed at that residue.</p>
+	<p>
+		Jalview visualises PAE matrices as an alignment annotation track,
+		shaded from dark green to white, similar to the encoding used on the
+		EBI-AlphaFold website (see <a
+			href="https://alphafold.ebi.ac.uk/entry/O04090">O04090 3D model</a>
+		at EBI-AlphaFoldDB).
+	</p>
 	<p>
 		<strong>Importing PAE Matrices</strong>
 	</p>
@@ -55,22 +64,23 @@
 		annotated with PAE matrices and PLDDT scores.
 	</p>
 	<p>
-		See <a href="../features/paematrices.html">Working with PAE
-			Matrices</a> for information on how they are visualised and analysed in
-		Jalview.
-	</p>
+		<strong>Showing PAE Matrix Annotations </strong>
 	</p>
 	<p>
-		An additional <em>Predicted Alignment Error</em> file can also be
-		provided when importing 3D structure data. Jalview supports import of
-		PAE Matrices provided as <a href="../io/paematrixformat.html">AlphaFold
-			format JSON files</a> - which are also produced by ColabFold. See <a
-			href="paematrices.html">Working with PAE Matrices</a> for details on
-		what Jalview allows you to do with associated PAE matrix data.
+		When viewing 3D structures from the EBI-AlphaFold database or local 3D
+		structures with an associated PAE file, the PAE is imported as <i>Reference
+			Annotation</i>, which is not always automatically added to the alignment
+		view.
 	</p>
+	<p>To show the PAE, right click the sequence and locate the 'Add
+		Reference Annotation' entry in the Sequence ID submenu, or select all
+		sequences and locate the option in the Selection submenu. You can do
+		this in any alignment window (or view) where a sequence with
+		associated PAE data appears.</p>
+	<p></p>
 	<p>
-		<em>The Structure Chooser interface was introduced in Jalview
-			2.9. </em>
+		<em>Support for visualision and analysis of predicted alignment
+			error matrices was added in Jalview 2.11.3. </em>
 	</p>
 </body>
 </html>