Working with Predicted Alignment Error Matrices in Jalview

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.

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 O04090 3D model at EBI-AlphaFoldDB).

Importing PAE Matrices

Jalview retrieves PAE matrices when importing predicted 3D structures from the EBI-AlphaFold database via Jalview's structure chooser 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 Load PDB File dropdown menu in the 3D structure chooser, providing it is in a supported PAE format.

The Command Line Interface 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.

Showing PAE Matrix Annotations

When viewing 3D structures from the EBI-AlphaFold database or local 3D structures with an associated PAE file, the PAE is imported as Reference Annotation, which is not always automatically added to the alignment view.

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.

Adjusting the height of PAE matrix annotations

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 SHIFT whilst doing this to adjust the height of all PAE rows at once.

PAE matrix annotation rows behave like any other sequence associated annotation, with the following additional features:

• The vertical axis of the PAE heatmap is mapped to positions on the linked 3D structure.
  • 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.
  • Clicking to select positions in the matrix results in columns of the alignment corresponding to the row and columns selected in the matrix.

  Clustering PAE Matrices

  Support for visualision and analysis of predicted alignment error matrices was added in Jalview 2.11.3.