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<body>
<p>
- Welcome to Jalview Version $$Version-Rel$$ !!<br />Please take a
+ <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.
+ notes</a> for this build. Read on for the highlights.
</p>
<p>
- <strong>Jalview 2.11.1.4</strong>
- </p>
- <p>Jalview 2.11.1.4 is the fourth patch release in the 2.11.1
- series. One critical bug was fixed in this release - when Jalview
- would occasionally hang when viewing structures in Jmol. This release
- also introduces a number of new configuration options for disabling
- web service connections used by the Jalview Debian package.
- </p>
- <p>
- For the full release notes, see <a
- href="releases.html#Jalview.2.11.1.4">the Jalview 2.11.1.4
- release notes</a>.
+ <strong>Highlights in 2.11.2</strong>
</p>
<p>
- <strong>Known Issues</strong>
- </p>
- <p>New known issues in this release affect recovery of CDS/Protein
- relationships from project files, and interactive selection of
- protein sequences from a tree built on linked nucleotide sequences.
- We will provide patches for these issues as soon as possible.</p>
+ <strong>New features for working with 3D Structure</strong><br />
+ Jalview 2.11.2 features a number of new capabilities:
+
+ <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
+ release notes</a>.
+ </p>
+ <p>
+ <strong>Known Issues</strong>
+ </p>
+ <p></p>
</ul>
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git://source.jalview.org / jalview.git / blobdiff