From 3ff0d70b248749cdf55048b8f13fc3e2e011c1d2 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 17 Feb 2022 12:58:37 +0000
Subject: [PATCH] JAL-3746 more release notes and docs: JAL-3863 JAL-3745

---
 help/help/html/features/chimera.html          |    2 +-
 help/help/html/features/pymol.html            |    4 +-
 help/help/html/features/structurechooser.html |   36 ++++++-------
 help/help/html/releases.html                  |    8 ++-
 help/help/html/whatsNew.html                  |   72 ++++++++++++++++++-------
 5 files changed, 80 insertions(+), 42 deletions(-)

diff --git a/help/help/html/features/chimera.html b/help/help/html/features/chimera.html
index eadfa06..6edc155 100644
--- a/help/help/html/features/chimera.html
+++ b/help/help/html/features/chimera.html
@@ -31,7 +31,7 @@
     (http://www.cgl.ucsf.edu/chimera/) can be used for viewing
     structures opened via the <a href="structurechooser.html"><strong>&quot;View
     Structure Data..&quot;</strong> dialog</a>. In Jalview 2.11.2, support 
-    was also added for ChimeraX.
+    was also added for ChimeraX, and <a href="pymol.html">Pymol</a>.
   </p>
   <p>
     You can set a default choice of Jmol or Chimera structure viewer in
diff --git a/help/help/html/features/pymol.html b/help/help/html/features/pymol.html
index 573310a..2c5c7ad 100644
--- a/help/help/html/features/pymol.html
+++ b/help/help/html/features/pymol.html
@@ -48,7 +48,7 @@
   <p>
     <strong>Jalview requires Pymol V 2.5.0 (community edition)
       or later</strong> <br />Jalview requires Pymol's RPC interface, which is
-    not available in older versions of the Pymol community edition.
+    not available in older versions of the Pymol community edition. 
   </p>
   <p>
     <strong>Known Limitations</strong><br />
@@ -61,7 +61,7 @@
       properties or highlighting sequence regions corresponding to
       structure selections or mouse-overs in Pymol.</li>
     <li>Jalview to Pymol communication currently doesn't highlight
-      the positions on structures corresponging to moused over residues
+      the positions on structures corresponding to moused-overs
       in Jalview.</li>
   </ul>
   <p>
diff --git a/help/help/html/features/structurechooser.html b/help/help/html/features/structurechooser.html
index 11cad6b..512b68f 100644
--- a/help/help/html/features/structurechooser.html
+++ b/help/help/html/features/structurechooser.html
@@ -91,16 +91,17 @@
     <strong>Selection of the best structure for each sequence</strong>
   </p>
   <p>Jalview can automatically select the best structures according
-    to meta-data provided by the PDB. For alignments with no existing
-    structure data, the 'PDBe Best Quality' structure for each sequence will
-    by default be selected, but clicking on the drop down menu allows
-    other criteria to be chosen, including Resolution (only defined for
-    X-Ray structures), Highest Protein Chain etc. When 'Invert' is
+    to meta-data provided by the search service. The 'PDBe Best Quality' structure for each sequence will
+    by default be selected when no other structure data is available. If 3D-models from other sources are also available, then 'Best 3D Beacons coverage' will be show.
+    <br/><br/>Clicking on the drop down menu allows
+    other criteria to be chosen. For the PDBe, these include including Resolution (only defined for
+    X-Ray structures), Highest Protein Chain etc. When 3D-Beacons results are available, structures can be selected based on their specific provider, or by their coverage of the aligned sequences.<br/>
+    <br/>When 'Invert' is
     selected, structures are selected in reverse order for the current
     criteria (e.g. worst quality rather than best).</p>
   <p>
 
-    <img src="schooser_main.png" style="width: 499px; height: 437px;">
+    <img src="schooser_main.png" style="width: 820px; height: 458px;">
     <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
 	<p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
 	<p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
@@ -125,16 +126,13 @@
     <br/>
     The 3D-Beacons Network search requires UniProt references and Jalview will ask
     to attempt to fetch these references for the selected sequences.
-    UniProt references might not always be found in which case you can revert to the PDB
-    search.
+    If no UniProt references are found, Jalview will still search the PDB for potential matches for the sequence's ID string.
     <br/>
     <img src="3dbeacons_structurechooser.png"/>
     <br/>
-    If structures are found through the 3D-Beacons network you can filter which structures
-    are shown using the drop-down filter at the top of the Structure Chooser window.
-    <br/>
+    Structures found through the 3D-Beacons network can be filtered using the drop-down filter at the top of the Structure Chooser window. 
     You can view information about each related model, such as the resource providing
-    each model, in the columns displayed. You can sort the list of models by clicking on
+    each model, in the displayed columns, and models can be reordered by clicking on
     column headings.
     <br/>
     Select and view the structures in the usual way using the <a href="viewingpdbs.html#afterviewbutton">open structure options</a> at
@@ -146,15 +144,15 @@
   </p>
   <p>Information on each structure available is displayed in columns
     in the dialog box. By default, only the title, resolution and PDB
-    identifier are shown, but many more are provided by the PDBe. To
-    configure which ones are displayed, select the 'Configure Displayed
-    Columns' tab and tick the columns which you want to see.</p>
+    identifier are shown, but many more are provided by the PDBe.
+    3D-Beacons structures have different data, including a quality score
+    (such as Qmeans_DISCO). To configure which ones are displayed,
+    select the 'Configure Displayed Columns' tab and tick the columns
+    which you want to see.</p>
   <p>
     <img src="schooser_enter-id.png"
-      style="width: 464px; height: 173px;">
-      <br/>
-    <strong>Manual selection/association of PDB files with
-      Sequences</strong>
+      style="width: 464px; height: 173px;"> <br /> <strong>Manual
+      selection/association of PDB files with Sequences</strong>
   </p>
   <p>To manually associate PDB files with a sequence, select 'From
     File', or 'Enter PDB Id' from the drop-down menu:
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 5e38f4b..a8d346b 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -63,7 +63,10 @@ li:before {
       <td align="left" valign="top">
         <ul>
           <li>
-            <!-- -->
+            <!-- JAL- -->
+          </li>
+          <li>
+            <!-- JAL-3863 -->Support for Canonical Uniprot IDs
           </li>
         </ul> <em>JalviewJS</em>
         <ul><li><!-- 3624 -->PDB structures mapped to Uniprot Sequences with SIFTS</li>
@@ -93,7 +96,8 @@ li:before {
           <li><!-- JAL-2848 -->Cancel from Amend Features doesn't reset a modified graduated colour</li>
         </ul> <em>Development</em>
         <ul>
-          <li>Fixed non-fatal gradle errors during build</li>
+          <li>Gradle<ul><li>Fixed non-fatal gradle errors during build</li>
+          <li><!--  JAL-3745 -->Updated build.gradle for use with Gradle v.6.6+</li></ul></li>
            
         </ul>
       </td>
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index 0cf5661..4e7be71 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -32,25 +32,61 @@
   <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>
-- 
1.7.10.2