</head>
<body>
<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 in the 2.11.1
- series. Critical bugs resolved in this release include:</p>
- <ul>
- <li>Find doesn't highlight all motif matches for a sequence.</li>
- <li>Mouse over highlighting, CDS reconstruction and problems
- with virtual feature popups when working with linked CDS/Protein
- alignments.</li>
- <li>Result of aligning protein sequences linked to CDS results
- in incorrect CDS alignment.</li>
- <li>Jalview installer doesn't correctly install Jalview on
- paths containing spaces.</li>
- </ul>
<p>
- For the full release notes, see <a
- href="releases.html#Jalview.2.11.1.3">the Jalview 2.11.1.3
- release notes</a>.
+ <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 described
+ below.
+ </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>Known Issues</strong>
+ <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. 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.<br />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.
</p>
+ <p>Other highlights include:</p>
<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>Easier configuration of <a
+ href="features/preferences.html#startup">Jalview's memory
+ allocation</a></strong></li>
+ <li>Import of annotated DNA and RNA loci via GenBank and EMBL
+ style flatfile</li>
+ <li>New <strong>command line launcher scripts</strong> (.sh, .ps1, .bat) usable on
+ macOS, Linux/Unix, Windows and documentation in Help
+ </li>
+
+
+
+
+ <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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</html>
git://source.jalview.org / jalview.git / blobdiff