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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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+ -->
+<head>
+<title>Working with PAE Matrices in Jalview</title>
+</head>
+
+<body>
+ <p>
+ <strong>Working with Predicted Alignment Error Matrices in
+ Jalview</strong>
+ </p>
+
+ <p>Predicted Alignment Error matrices are produced by deep-learning
+ based 3D-structure prediction pipelines such as AlphaFold.</p>
+ <p>
+ Jalview retrieves PAE matrices when importing predicted 3D structures
+ from the EBI-AlphaFold database via <a
+ href="../features/structurechooser.html">Jalview's structure
+ chooser</a> GUI.
+ </p>
+ <p>
+ 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 <a href="../features/structurechooser.html#loadpdbfile">Load
+ PDB File</a> dropdown menu in the 3D structure chooser, providing it is
+ in a <a href="../io/paematrixformat.html">supported PAE format</a>. ,
+ or the <a href="../features/clarguments-basic.html">Command Line
+ Interface</a>. See <a href="../features/paematrices.html">Working
+ with PAE Matrices</a> for information on how they are visualised and
+ analysed in Jalview.
+ </p>
+ </p>
+ <p>
+ An additional <em>Predicted Alignment Error</em> file can also be
+ provided when importing 3D structure data. Jalview supports import of
+ PAE Matrices provided as <a href="../io/paematrixformat.html">AlphaFold
+ format JSON files</a> - which are also produced by ColabFold. See <a
+ href="paematrices.html">Working with PAE Matrices</a> for details on
+ what Jalview allows you to do with associated PAE matrix data.
+ </p>
+ <p>
+ <em>The Structure Chooser interface was introduced in Jalview
+ 2.9. </em>
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff