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<p>
- <strong>Jalview 2.11.1.3</strong>
+ <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>Jalview 2.11.1.3 is the third patch release, fixing a bug
- introduced in last weeks Jalview 2.11.1.1 release affecting display
- of Jalview's example project for some users. Together, these
- releases include fixes for a number of critical bugs, and also contains a
- handful of new features suggested by the Jalview community.</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>
- <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>.
+ <strong>Highlights in 2.11.2</strong>
</p>
<p>
- <strong>Known Issues</strong>
- </p>
+ <strong>New features for working with 3D Structure</strong><br />
+ Jalview 2.11.2 features a number of new capabilities:
+
<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><strong>Linked viewing with <em>ChimeraX</em> and
+ <em>PyMol</em></strong><br />Simply configure your preferred 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>
+ <li><strong>Easier configuration of <a href="features/preferences.html#startup">Jalview's memory allocation</a></strong>
+ <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
+ release notes</a>.
+ </p>
+ <p>
+ <strong>Known Issues</strong>
+ </p>
+ <p></p>
</ul>
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git://source.jalview.org / jalview.git / blobdiff