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 (file)
--- 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>