From: James Procter <j.procter@dundee.ac.uk>
Date: Mon, 25 Sep 2023 16:55:38 +0000 (+0100)
Subject: JAL-3858 JAL-4090 PAE documentation..
X-Git-Tag: Release_2_11_4_0~163
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c10d8000dd752b76576db162dcd3d1e1925c0704;p=jalview.git

JAL-3858 JAL-4090 PAE documentation..
---

diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html
index cebc16b..e883bdb 100644
--- a/help/help/html/features/paematrices.html
+++ b/help/help/html/features/paematrices.html
@@ -29,24 +29,35 @@
 			Jalview</strong>
 	</p>
 
-	<p>Predicted Alignment Error matrices are produced by deep-learning
-		based 3D-structure prediction pipelines such as AlphaFold.</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>
+		<strong>Importing PAE Matrices</strong>
+	</p>
 	<p>
 		Jalview retrieves PAE matrices when importing predicted 3D structures
 		from the EBI-AlphaFold database via <a
 			href="../features/structurechooser.html">Jalview's structure
-			chooser</a> GUI.
+			chooser</a> GUI. If you have produced your own models and accompanying
+		PAE matrices using a pipeline such as ColabFold, then you can load
+		them both together via the <a
+			href="../features/structurechooser.html#loadpdbfile">Load PDB
+			File</a> dropdown menu in the 3D structure chooser. in a <a
+			href="../io/paematrixformat.html">supported PAE format</a>.
+	</p>
+	<p>
+		The <a href="../features/clarguments-basic.html">Command Line
+			Interface</a> also provides a options for importing PAE matrices along
+		side models, enabling the automated production of alignment figures
+		annotated with PAE matrices and PLDDT scores.
 	</p>
 	<p>
-		If you have produced your own models using a pipeline such as
-		ColabFold, then you can load it via the 'Add PAE matrix file' button
-		in the <a href="../features/structurechooser.html#loadpdbfile">Load
-			PDB File</a> dropdown menu in the 3D structure chooser, providing it is
-		in a <a href="../io/paematrixformat.html">supported PAE format</a>. ,
-		or the <a href="../features/clarguments-basic.html">Command Line
-			Interface</a>. See <a href="../features/paematrices.html">Working
-			with PAE Matrices</a> for information on how they are visualised and
-		analysed in Jalview.
+		See <a href="../features/paematrices.html">Working with PAE
+			Matrices</a> for information on how they are visualised and analysed in
+		Jalview.
 	</p>
 	</p>
 	<p>