JAL-3746 more release notes and docs: JAL-3863 JAL-3745

[jalview.git] / help / help / html / whatsNew.html

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   <p>
     <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:<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
-  </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>.
-  </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> 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. 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>).
+    </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>.
+    </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>
   </ul>
 </body>
 </html>