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<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.
+ <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong><br/>
</p>
+<p>Jalview 2.11.2.2 is the second patch release in the 2.11.2 series.</p>
+
<p>
- <strong>Highlights in 2.11.2</strong>
+ 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>New features for working with 3D Structure</strong><br />
- Jalview 2.11.2 features a number of new capabilities:
-
+ <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><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> 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>).
- The 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.
- </p>
- <p>
- For the full release notes, see <a
- href="releases.html#Jalview.2.11.2.0">the Jalview 2.11.2.0
+ <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>
- </p>
- <p></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>
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