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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 <a
60 href="../features/structurechooser.html#loadpdbfile">Load PDB
61 File</a> dropdown menu in the 3D structure chooser. in a <a
62 href="../io/paematrixformat.html">supported PAE format</a>.
65 The <a href="../features/clarguments-basic.html">Command Line
66 Interface</a> also provides a options for importing PAE matrices along
67 side models, enabling the automated production of alignment figures
68 annotated with PAE matrices and PLDDT scores.
71 <strong>Showing PAE Matrix Annotations </strong>
74 When viewing 3D structures from the EBI-AlphaFold database or local 3D
75 structures with an associated PAE file, the PAE is imported as <i>Reference
76 Annotation</i>, which is not always automatically added to the alignment
79 <p>To show the PAE, right click the sequence and locate the 'Add
80 Reference Annotation' entry in the Sequence ID submenu, or select all
81 sequences and locate the option in the Selection submenu. You can do
82 this in any alignment window (or view) where a sequence with
83 associated PAE data appears.</p>
86 <em>Support for visualision and analysis of predicted alignment
87 error matrices was added in Jalview 2.11.3. </em>