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23 <title>Working with PAE Matrices in Jalview</title>
28 <strong>Working with Predicted Alignment Error Matrices in
32 <p>Predicted Alignment Error (PAE) matrices are produced by
33 deep-learning based 3D-structure prediction pipelines such as
34 AlphaFold. They reflect how reliably two parts of a model have been
35 positioned in space, by giving for each residue the likely error (in
36 Ångstroms) between that residue and every other modelled
37 position the pair of residues' real relative position, if the model
38 and real 3D structure were superimposed at that residue.</p>
40 Jalview visualises PAE matrices as an alignment annotation track,
41 shaded from dark green to white, similar to the encoding used on the
42 EBI-AlphaFold website (see <a
43 href="https://alphafold.ebi.ac.uk/entry/O04090">O04090 3D model</a>
46 <div style="display:flex; flex-wrap:wrap;"align="center" width="100%">
47 <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>
48 <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>
51 <strong>Importing PAE Matrices</strong>
54 Jalview retrieves PAE matrices when importing predicted 3D structures
55 from the EBI-AlphaFold database via <a
56 href="../features/structurechooser.html">Jalview's structure
57 chooser</a> GUI. If you have produced your own models and accompanying
58 PAE matrices using a pipeline such as ColabFold, then you can load
59 them both together via the
60 <a href="../features/structurechooser.html#loadpdbfile">Load PDB
61 File</a> dropdown menu in the 3D structure chooser, providing it is
63 <a href="../io/paematrixformat.html">supported PAE format</a>.
66 The <a href="../features/clarguments-basic.html">Command Line
67 Interface</a> also provides a options for importing PAE matrices along
68 side models, enabling the automated production of alignment figures
69 annotated with PAE matrices and PLDDT scores.
72 <strong>Showing PAE Matrix Annotations </strong>
75 When viewing 3D structures from the EBI-AlphaFold database or local 3D
76 structures with an associated PAE file, the PAE is imported as <i>Reference
77 Annotation</i>, which is not always automatically added to the alignment
80 <p>To show the PAE, right click the sequence and locate the 'Add
81 Reference Annotation' entry in the Sequence ID submenu, or select all
82 sequences and locate the option in the Selection submenu. You can do
83 this in any alignment window (or view) where a sequence with
84 associated PAE data appears.</p>
87 <em>Support for visualision and analysis of predicted alignment
88 error matrices was added in Jalview 2.11.3. </em>