+ Supported Formats for Predicted Alignment Error + Matrices +
++ Predicted Alignment Error matrices are square matrices produced as + part of deep-learning based 3D-structure prediction pipelines such as + AlphaFold. They can be imported via Jalview's structure + chooser GUI and the Command + Line Interface. See Working + with PAE Matrices for information on how they are visualised and + analysed in Jalview. +
++ Supported Formats +
+Jalview supports import of PAE matrix data as provided by the + EBI-AlphaFold database. This resource provides PAE matrices as a JSON + files structured in one of the following ways:
+
+ # Version 1 format PAE file - deprecated 28th July 2022
+ {
+ residue1:[1,1,... total number of residues]
+ residue2:[1,2,... total number of residues]
+ distance:[0.1,0.3,... list of PAE matrix elements as doubles]
+ }
+
+
+ # Version 2 format PAE file - see https://alphafold.ebi.ac.uk/faq
+ {
+ max_predicted_alignment_error: 4.0, # may also be max_pae
+ predicted_alignment_error: [[1,2,0,0,3,...],...] # may also be pae
+ }
+
+
+ Variants of the version 2 format include using 'pae' instead of
+ 'predicted_alignment_error' in the names of keys. Jalview copes both.
+ Once imported, Jalview stores PAE matrices as float arrays along with
+ any associated tree and partition set resultant from clustering the
+ matrix.
PAE Matrix import support was added in Jalview 2.11.3
+
+