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23 <title>Supported Formats for Predicted Alignment Error Matrices</title>
28 <strong>Supported Formats for Predicted Alignment Error
32 Predicted Alignment Error matrices are square matrices produced as
33 part of deep-learning based 3D-structure prediction pipelines such as
34 AlphaFold. They can be imported via <a
35 href="../features/structurechooser.html">Jalview's structure
36 chooser</a> GUI and the <a href="../features/clarguments-basic.html">Command
37 Line Interface</a>. See <a href="../features/paematrices.html">Working
38 with PAE Matrices</a> for information on how they are visualised and
42 <strong>Supported Formats</strong>
44 <p>Jalview supports import of PAE matrix data as provided by the
45 EBI-AlphaFold database. This resource provides PAE matrices as a JSON
46 files structured in one of the following ways:</p>
48 # Version 1 format PAE file - deprecated 28th July 2022
50 residue1:[1,1,... total number of residues]
51 residue2:[1,2,... total number of residues]
52 distance:[0.1,0.3,... list of PAE matrix elements as doubles]
56 # Version 2 format PAE file - see https://alphafold.ebi.ac.uk/faq
58 max_predicted_alignment_error: 4.0, # may also be max_pae
59 predicted_alignment_error: [[1,2,0,0,3,...],...] # may also be pae
63 Variants of the version 2 format include using 'pae' instead of
64 'predicted_alignment_error' in the names of keys. Jalview copes both.<br />
65 Once imported, Jalview stores PAE matrices as float arrays along with
66 any associated tree and partition set resultant from clustering the
67 matrix. <br/><br/><em>PAE Matrix import support was added in Jalview 2.11.3