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. Each column in a PAE matrix corresponds to a
+ residue in the model, and each gives the likely RMS 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>
+ <img src="../structures/epas1_annotdetail.png" width="450" />
+ <br/><em>
+ Alignment of EPAS1 homologs from Human, Rat and Cow shaded by PLDDT, with
+ Predicted Alignment Error and secondary structure annotation shown for Human.
+ </em>
+ <!--</div>
+ <div width="35%">
+ <figure>
+ <img src="../structures/epas1_pae_ebiaf.png" />
+ <figcaption>
+ Predicted Alignment Error for Human EPAS1<br />from <a
+ href="https://alphafold.ebi.ac.uk/entry/Q99814">https://alphafold.ebi.ac.uk/entry/Q99814</a>
+ </figcaption>
+ </figure>
+ </div>
+ </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, providing it is 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 the option to import a PAE matrix alongside
+ a 3D structure file, 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>, and 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>
- 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 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>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>Mousing over the matrix shows a tooltip giving information
+ on the range of values under the mouse.<br />Positions in the
+ associated 3D structure are also highlighted in any linked views.
+ </li>
+ <li>Clicking on positions in the matrix selects columns of the
+ alignment corresponding to the row and column in the matrix.</li>
+ </ul>
+ </li>
+ <li>Rectangular selections (created by Cmd (or Alt)+Click
+ dragging on the matrix) can be created to select multiple ranges of
+ columns at once.</li>
+ <li>Columns corresponding to adjacent regions with similarly low
+ levels of predicted alignment error can be selected by Ctrl+Clicking
+ on a region in the matrix.</li>
+ <li>Columns of an alignment showing a PAE matrix can be grouped
+ and selected by clustering the matrix.</li>
+ </ul>
+ <p>
+ <strong><a name="clustering">Clustering PAE Matrices</a></strong>
+ </p>
+ <p>PAE matrices are useful for identifying regions of 3D structure
+ predictions that are likely to be positioned in space in the same or
+ similar way as shown in the predicted structure data. Regions of low
+ PAE often correlate with high alphafold reliability (PLDDT) scores,
+ but also complement them since they highlight well-folded regions such
+ as domains, and how well those regions have been predicted to be
+ positioned relative to each other, which is important when evaluating
+ whether domain-domain interactions or other contacts can be trusted.</p>
+ <p>To make it easy to identify regions of low PAE, Jalview can
+ cluster the PAE matrix, allowing columns of the matrix to be grouped
+ according to their similarity, using an Average Distance (UPGMA) tree
+ algorithm and the sum of differences between each column's PAE values.</p>
+ <p>
+ <strong><em>dist<sub>ij</sub></em> = ∥ <em><u>p</u><sub>i</sub>-<u>p</u><sub>j</sub></em>
+ ∥</strong>
+ </p>
+ <p>
+ <em>Creating a PAE matrix tree</em><br/>Right click on a PAE annotation's label
+ to open the annotation popup menu, and select <strong><em>Cluster
+ Matrix</em></strong>. Once the calculation has finished, a tree viewer will open,
+ and columns of the matrix are then partitioned into groups such that
+ the third left-most node from the root is placed in its own group.
+ Colours are randomly assigned to each group. By default column group colours will
+ also be overlaid on the matrix annotation row - this can be turned off
+ via the PAE annotation row menu (by unticking <em>Show groups on matrix</em>).</p>
+ <p>
+ The PAE matrix tree viewer behaves like other tree views, except:
+ <ul>
+ <li>Selecting nodes or groups of nodes in the tree select
+ columns in the alignment, and clicking in the tree window adjust
+ the matrix's partition.</li>
+ <li>Only one tree and clustering can be defined for a PAE matrix,
+ regardless of whether it is displayed in different views or
+ alignments.</li>
+ </ul>
+ Once the PAE annotation has clustering defined:
+ <ul><li>Double clicking on a position in the PAE annotation where a
+ clustering has been defined will select both the row and column
+ clusters for the clicked position. <br/><br/>This makes it easy to select
+ clusters corresponding to pairs of interacting regions.</li>
+ <li>Cluster colours for a PAE matrix can be used to colour
+ sequences or columns of the alignment via the <strong><em><a
+ href="../colourSchemes/annotationColouring.html">Colour by
+ Annotation.. dialog</a></em></strong>
+ (opened by right-clicking the annotation label
+ and selecting from the popup menu).
+ </li>
+ </ul>
+ <p>
+ <strong>PAE matrices and Jalview Projects</strong>
</p>
+ <p>Any PAE matrices imported to Jalview are saved along side any
+ trees and clustering defined on them in Jalview Projects.</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