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

diff --git a/help/help/html/features/chimera.html b/help/help/html/features/chimera.html
index eadfa06..6edc155 100644 (file)
--- 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 
     (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
   </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 (file)
--- 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
   <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 />
   </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
       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>
       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 (file)
--- 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
     <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>
 
     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; ">
     <!-- <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.
     <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/>
     <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
     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
     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
   </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"
   <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:
   </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 (executable)
--- 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>
       <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>
           </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><!-- 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>
            
         </ul>
       </td>

diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index 0cf5661..4e7be71 100755 (executable)
--- 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>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>
   <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>

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