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<p>
- <strong>Jalview 2.11.1.1</strong>
+ <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong><br/>
</p>
- <p>Jalview 2.11.1.1 is the first patch release for Jalview version
- 2.11.1. In addition to fixes for some critical bugs, it also
- contains a handful of new features suggested by the Jalview
- community.</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>Shift+arrow keys navigate to next gap or residue in cursor
- mode (enable with F2)</li>
- <li>Support import of VCF 4.3 by updating HTSJDK from 2.12 to
- 2.23</li>
- <li>Improved recognition of GZipped files from local disk or
- retrieved via the web</li>
- <li>EMBL and EMBL CDS database records retrieved from the
- European Nucleotide Archive's Data API as 'EMBL Flatfile' records</li>
- <li>Improved <a href="logging.html">Java Console and
- logging</a> to help track down problems
+ <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>
- <li>Improved support for Hi-DPI (4K) screens when running on
- Linux (Requires Java 11+)</li>
- </ul>
- <p>Critical bug fixes include</p>
- <ul>
- <li>Jalview runs correctly when launched with Turkish language
- settings</li>
- <li>Peptide-to-CDS tracking broken when multiple EMBL gene
- products shown for a single contig (such as viral genomes)</li>
- <li>Errors encountered when processing variants from VCF files
- yield "Error processing VCF: Format specifier '%s'" on the console</li>
- <li>Count of features not shown can be wrong when there are
- both DNA and Protein features mapped to the position under
- the cursor</li>
- <li>Sequence ID for reference sequence is clipped when Right
- align Sequence IDs enabled</li>
- <li>Find doesn't report matches that span hidden gapped columns</li>
- <li>Jalview ignores file format parameter specifying output
- format when exporting an alignment via the command line</li>
</ul>
+
+
<p>
- For the full release notes, see <a href="releases.html#Jalview.2.11.1.1">the
- Jalview 2.11.1.1 release notes</a>.
- </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>
+ <strong>Known Issues</strong> <br />The following known issues will
+ be addressed in a minor patch release.
+
<ul>
- <li>We've had reports from a small number of windows 10 users
- who see a warning dialog pop up when Jalview tries to save a new
- version of an existing file. If you are affected by this bug and
- this latest version of Jalview doesn't fix it, please let us know!</li>
- <li>Co-located features exported and re-imported are ordered
- differently when shown on alignment and in tooltips. (Also affects
- v2.11.1.0)</li>
- <li>Drag and drop of alignment file onto alignment window when
- in a HiDPI scaled mode in Linux only works for the top left
- quadrant of the alignment window</li>
+ <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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git://source.jalview.org / jalview.git / blobdiff