From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 28 Feb 2022 17:57:49 +0000 (+0000)
Subject: JAL-3746 JAL-3551 update pymol docs and what’s new text
X-Git-Tag: Release_2_11_2_1~58
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=63747d835b0d6b1e4b3d3d5dd99561af191ee1a9

JAL-3746 JAL-3551 update pymol docs and what’s new text
---

diff --git a/help/help/html/features/pymol.html b/help/help/html/features/pymol.html
index 2c5c7ad..c6a2ae2 100644
--- a/help/help/html/features/pymol.html
+++ b/help/help/html/features/pymol.html
@@ -59,10 +59,7 @@
       example project).</li>
     <li>Pymol to Jalview communication does not support transfer of
       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 corresponding to moused-overs
-      in Jalview.</li>
+      structure selections or mouse-overs in Pymol.</li>      
   </ul>
   <p>
     Basic screen operations (see <a
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index 4e7be71..f529c56 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -64,29 +64,26 @@
     </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
+        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.2.11.1.4">the Jalview 2.11.1.4
+        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>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>
+    <p></p>
   </ul>
 </body>
 </html>