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 Angstroms) between the modelled position and the pair of residues' real relative position.

Jalview visualises PAE matrices as an alignment annotation track, shaded from dark green to white, as used on the EBI-AlphaFold website (see )

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. 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.

See Working with PAE Matrices for information on how they are visualised and analysed in Jalview.

An additional Predicted Alignment Error file can also be provided when importing 3D structure data. Jalview supports import of PAE Matrices provided as AlphaFold format JSON files - which are also produced by ColabFold. See Working with PAE Matrices for details on what Jalview allows you to do with associated PAE matrix data.

The Structure Chooser interface was introduced in Jalview 2.9.