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
+ Ångstroms) 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>
<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>
- 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.
+ 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>
+ <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>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff