--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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>
style="width: 464px; height: 173px;"> <br /> <strong>Manual
selection/association of PDB files with Sequences</strong>
</p>
- <p>To manually associate PDB files with a sequence, select 'From
- File', or 'Enter PDB Id' from the drop-down menu:
- <ul>
- <li><strong>From File</strong> - allows you to load a PDB file
- from the local machine or network and associate it with the
- selected sequence. PDB files associated in this way will also be
- saved in the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
- <li><strong>Enter PDB Id</strong> - allows you specify a PDB ID
- for your sequence. The PDB Rest API, provided by EMBL-EBI, is used
- to validate and fetch structure data.<br></li>
- </ul>
-
- <p>
- <em>The Structure Chooser interface was introduced in Jalview
- 2.9. </em>
- </p>
+ <p>
+ <strong>Manual Association of PDBe accessions with sequences</strong>
+ </p>
+ <p>If for some reason the PDBe and 3D beacons search fail to
+ automatically the PDB structure or model you wish to import, you can
+ select 'Enter PDB Id' from the drop-down menu to manually specify PDB
+ identifiers for one or more selected sequences. The PDB Rest API,
+ provided by EMBL-EBI, is used to validate accessions exist, and fetch
+ structure data.</p>
+ <p>
+ <strong><a name="loadpdbfromfile">Import structure models
+ and metadata from file</a></strong>
+ </p>
+ <p>
+ Selecting the <strong>From File</strong> option from the drop down
+ menu allows 3D structure data to be imported from your own computer.
+ PDB or mmCIF files associated in this way are also saved in <a
+ href="jalarchive.html">Jalview Projects</a>. <br /> <img
+ src="local-pdb-import.png" style="width: 496px; height: 482px;"><br />
+ The 'From File' dialog provides a drop down menu which allows you to
+ specify how the Temperature Factor metadata for each residue in the 3D
+ structure data file is interpreted:
+
+ <ul>
+ <li>Default - Jalview will try to automatically determine whether
+ to show as 'Temperature Factor', 'AlphaFold Reliability' or 'Model
+ Quality'</li>
+ <li>PLDDT - Model has PLDDT scores in the temperature factor
+ column.</li>
+ </ul>
+ <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>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Supported Formats for Predicted Alignment Error Matrices</title>
+</head>
+
+<body>
+ <p>
+ <strong>Supported Formats for Predicted Alignment Error
+ Matrices</strong>
+ </p>
+ <p>
+ 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 <a
+ href="../features/structurechooser.html">Jalview's structure
+ chooser</a> GUI and 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>
+ <strong>Supported Formats</strong>
+ </p>
+ <p>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:</p>
+ <pre>
+ # 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]
+ }
+ </pre>
+ <pre>
+ # 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
+ }
+ </pre>
+ <p>
+ Variants of the version 2 format include using 'pae' instead of
+ 'predicted_alignment_error' in the names of keys. Jalview copes both.<br />
+ Once imported, Jalview stores PAE matrices as float arrays along with
+ any associated tree and partition set resultant from clustering the
+ matrix. <br/><br/><em>PAE Matrix import support was added in Jalview 2.11.3
+ </em>
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff
