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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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-<head>
-<title>What's new ?</title>
-</head>
-<body>
- <p>
- <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong><br/>
- </p>
- <p><em>19 April 2022</em></p>
-<p>Jalview 2.11.2.2 is the second patch release in the 2.11.2 series.</p>
-
- <p>
- This release series provides support for two popular 3D
- structure visualisation tools, new features for discovery of 3D
- structures, improved platform integration and a new command line
- tool allowing Jalview to be more easily called from scripts.</p>
-
- <p>
- <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>. Launched in
- 2021, 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>
- </p>
-
- <p>
- <strong>Support for viewing structures with ChimeraX and
- Pymol</strong><br> 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>).<br /> <br />
- The <a href="features/preferences.html#structure">Structures
- Preferences tab</a> provides new options allowing ChimeraX and
- Pymol to be used for visualising external 3D structures. Views
- from all structure viewers are saved in Jalview Projects, allowing
- them to be shared with others using Jalview 2.11.2 or later,
- providing they have the same viewer installed and configured to be
- used with Jalview.<br/><br/>Jalview
- 2.11.2 has been tested with <strong>Pymol 2.5.0 (community)</strong> and <strong>2.5.2
- (incentive)</strong>. For <strong>ChimeraX, we recommend using v1.3 or later</strong>.
- </p>
- <p>Other highlights include:</p>
- <ul>
- <li>Import of annotated DNA and RNA loci via GenBank and EMBL
- style flatfile</li>
- <li><strong>Easier configuration of <a
- href="features/preferences.html#startup">Jalview's memory
- allocation</a></strong></li>
- <li>Scripts for <a href="features/commandline.html">running
- Jalview via the command line</a> on macOS, Linux/Unix and Windows.
- </li>
- </ul>
-
-
- <p>
- For the full details, see <a
- href="releases.html#Jalview.2.11.2.1">the Jalview 2.11.2.1
- release notes</a>.
- </p>
- <p>
- <strong>Known Issues</strong> <br />The following known issues will
- be addressed in a minor patch release.
-
- <ul>
- <li>Display of RESNUM sequence features are not suppressed when
- structures associated with a sequence are viewed with an external
- viewer (Regression from 2.11.1 series)</li>
- </ul>
- <p></p>
-</body>
-</html>
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