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- * 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.
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- * Jalview is distributed in the hope that it will be useful, but
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- * You should have received a copy of the GNU General Public License
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- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>What's new ?</title>
-</head>
-<body>
- <p>
- <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong>
- <br />Please take a
- look at the <a href="releases.html#Jalview.$$Version-Rel$$">release
- notes</a> for this build. Read on for the highlights.
- </p>
- <p>
- <strong>Highlights in 2.11.2</strong>
- </p>
- <p>
- <strong>New features for working with 3D Structure</strong><br />
- Jalview 2.11.2 features a number of new capabilities:
-
- <ul>
- <li><strong>Linked viewing with <em>ChimeraX</em> and
- <em>PyMol</em></strong><br />Simply configure your prefered viewer for 3D
- molecular data in <a href="features/preferences.html#structure">Jalview's
- structure preferences</a>, make sure that Jalview can locate the
- viewer's installation, and open a new view via the 3D Structure
- Chooser!</li>
- <li><strong>View predicted protein structures via
- 3D-Beacons</strong><br /> Jalview 2.11.2's <a
- href="features/structurechooser.html">Structure Chooser
- includes a client for the 3D-Beacons Network</a>, a new service that
- allows predicted and observed 3D models for proteins in Uniprot
- from a range of resources, including AlphaFold DB, SWISS-MODEL and
- a growing number of other resources.</li>
- <p>
- <strong>Retrieval of 3D models via 3D-Beacons</strong> <br>The
- 3D-Beacons network (<a
- href="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/">www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/</a>)
- provides a central point for the retrieval of predicted and
- observed 3D structures for sequences in Uniprot, including
- homology models from Swiss-model and deep learning based
- predictions from the EBI's Alphafold database (Orengo et al. 2020,
- <a href="https://doi.org/10.12688/f1000research.20559.1">doi:10.12688/f1000research.20559.1</a>).<br>
- See the <a href="features/structurechooser.html">Structure
- Chooser's documentation</a>.
- </p>
- <p>
- <strong>Support for viewing structures with ChimeraX and
- Pymol</strong><br> Structures Preferences tab provides new options
- allowing ChimeraX and Pymol to be used for visualising external 3D
- structures. Jalview 2.11.2 has been tested with Pymol 2.5.0
- (community) and 2.5.2 (incentive). For ChimeraX, we recommend
- using v1.3 or later. Jalview's 3D structure viewer system has been
- re-architected to allow easier integration of external structure
- viewers, and takes advantage of the strucViz2 Chimera
- communications library developed by Scooter Morris (<a
- href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).
- </p>
- <p>
- For the full release notes, see <a
- href="releases.html#Jalview.2.11.1.4">the Jalview 2.11.1.4
- release notes</a>.
- </p>
- <p>
- <strong>Known Issues</strong>
- </p>
- <p>New known issues in this release affect recovery of
- CDS/Protein relationships from project files, and interactive
- selection of protein sequences from a tree built on linked
- nucleotide sequences. We will provide patches for these issues as
- soon as possible.</p>
- </ul>
-</body>
-</html>
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