3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Working with PAE Matrices in Jalview</title>
28 <strong>Working with Predicted Alignment Error Matrices in
32 <p>Predicted Alignment Error matrices are produced by deep-learning
33 based 3D-structure prediction pipelines such as AlphaFold.</p>
35 Jalview retrieves PAE matrices when importing predicted 3D structures
36 from the EBI-AlphaFold database via <a
37 href="../features/structurechooser.html">Jalview's structure
41 If you have produced your own models using a pipeline such as
42 ColabFold, then you can load it via the 'Add PAE matrix file' button
43 in the <a href="../features/structurechooser.html#loadpdbfile">Load
44 PDB File</a> dropdown menu in the 3D structure chooser, providing it is
45 in a <a href="../io/paematrixformat.html">supported PAE format</a>. ,
46 or the <a href="../features/clarguments-basic.html">Command Line
47 Interface</a>. See <a href="../features/paematrices.html">Working
48 with PAE Matrices</a> for information on how they are visualised and
53 An additional <em>Predicted Alignment Error</em> file can also be
54 provided when importing 3D structure data. Jalview supports import of
55 PAE Matrices provided as <a href="../io/paematrixformat.html">AlphaFold
56 format JSON files</a> - which are also produced by ColabFold. See <a
57 href="paematrices.html">Working with PAE Matrices</a> for details on
58 what Jalview allows you to do with associated PAE matrix data.
61 <em>The Structure Chooser interface was introduced in Jalview