JAL-4090 more JAL-3858 docs

[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..8d72573 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>
@@ -55,22 +68,38 @@
                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.
+               <strong>Showing PAE Matrix Annotations </strong>
        </p>
+       <p>
+               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><strong>Adjusting the height of PAE matrix annotations</strong></p>
+         <p>PAE annotations behave in the same way as Jalview's line graph and histogram tracks. Click+dragging up and down with the left (select) mouse button held down will increase or decrease the height of the annotation. You can also hold down <strong><em>SHIFT</em></strong> whilst doing this to adjust the height of all PAE rows at once. 
+         </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.
+         PAE matrix annotation rows behave like any other sequence associated annotation, with the following additional features:
+       </p>
+       <ul>
+         <li>The vertical axis of the PAE heatmap is mapped to positions on the linked 3D structure.
+           <ul><li>Moving the mouse over any part of the heatmap highlights the corresponding regions of the 3D structure the PAE data is associated with, in addition to a tooltip being displayed giving information on the range of values under the mouse.</li>
+             <li>Clicking to select positions in the matrix results in columns of the alignment corresponding to the row and columns selected in the matrix.</li>
+       </ul>
+       <p></p>
+           <p><strong><a name="clustering">Clustering PAE Matrices</a></strong></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>
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