JAL-4090 JAL-3855 updated figure and doc.. a little

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

diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html
index e883bdb..8d180ee 100644 (file)
--- a/help/help/html/features/paematrices.html
+++ b/help/help/html/features/paematrices.html
@@ -29,11 +29,24 @@
                        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>
+       <div style="display:flex; flex-wrap:wrap;"align="center" width="100%">
+       <figure><img src="../structures/epas1_annotdetail.png" height="300"/><figcaption>Alignment of EPAS1 homologs from Human, Rat and Cow, with predicted alignment error shown in Jalview</figcaption></figure>
+       <figure><img src="../structures/epas1_pae_ebiaf.png" height="300"/><figcaption>Predicted Alignment Error Matrix<br/>from <a href="https://alphafold.ebi.ac.uk/entry/Q99814">https://alphafold.ebi.ac.uk/entry/Q99814</a></figcaption></figure>
+       </div>
        <p>
                <strong>Importing PAE Matrices</strong>
        </p>
@@ -43,10 +56,11 @@
                        href="../features/structurechooser.html">Jalview's structure
                        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>.
+               them both together via 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>.
        </p>
        <p>
                The <a href="../features/clarguments-basic.html">Command Line
@@ -55,22 +69,23 @@
                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>