Working with Predicted Alignment Error Matrices in Jalview

Predicted Alignment Error matrices are produced by deep-learning based 3D-structure prediction pipelines such as AlphaFold.

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 using a pipeline such as ColabFold, then you can load it via the 'Add PAE matrix file' button in the Load PDB File dropdown menu in the 3D structure chooser, providing it is in a supported PAE format. , or the Command Line Interface. 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.