From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 9 Jun 2022 13:25:39 +0000 (+0100)
Subject: JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation
X-Git-Tag: Release_2_11_2_6~51
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a7634a9f5f5f691a7bff7bb05ca21a340aa2f834;p=jalview.git

JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation
---

diff --git a/help/help/html/features/pymol.html b/help/help/html/features/pymol.html
index c6a2ae2..7bf5651 100644
--- a/help/help/html/features/pymol.html
+++ b/help/help/html/features/pymol.html
@@ -218,11 +218,25 @@
       </ul></li>
   </ul>
   <p>
+    <strong>Troubleshooting</strong>
+  </p>
+  Jalview will try to automatically configure itself according to the
+  configured Pymol installation (or the first one it discovers in the
+  standard installation locations). You can see which Pymol executable
+  is being used by enabling
+  <em>DEBUG</em> output in
+  <a href="../logging.html">Jalview's Java console</a>.
+  <br />
+  <br />If Jalview raises warning messages about Pymol not being located
+  or executed, or no structures appear when Jalview launches Pymol,
+  please ask for help on
+  <a href="https://discourse.jalview.org">Jalview's discussion forum</a>.
+  <p>
     <strong>Pymol and Windows Firewall</strong>
   </p>
   Jalview and Pymol communicate using the
   <a href="https://pymolwiki.org/index.php/RPC">Pymol's XML-RPC over
-    HTTP interface</a>(https://pymolwiki.org/index.php/RPC).
+    HTTP interface</a> (https://pymolwiki.org/index.php/RPC).
 
   <br> Technically this requires both Pymol and Jalview to open
   ports on the local network, and this may be blocked by Windows
diff --git a/help/markdown/releases/release-2_11_2_3.md b/help/markdown/releases/release-2_11_2_3.md
index 18449ad..99cb736 100644
--- a/help/markdown/releases/release-2_11_2_3.md
+++ b/help/markdown/releases/release-2_11_2_3.md
@@ -15,6 +15,7 @@ channel: "release"
 ## Issues Resolved
 
 - <!-- JAL-4008 --> Validation fails when trying to configure custom JABAWS server
+- <!-- JAL-4020 --> Jalview doesn't call PymolWIN.exe correctly - improved recognition of binaries on Windows
 - <!-- JAL-4024 --> Jumping from left to far right via rapid drag of scroll bar or clicking the overview window can cause Jalview to temporarily hang when working with alignments with more than 10 thousand columns
 - <!-- JAL-4023 --> Labels for tree branches smaller than 0.005 are shown as '0' in the tree viewer
 - <!-- JAL-1544 --> Fixed typos in documentation