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

[jalview.git] / help / help / html / features / pymol.html

diff --git a/help/help/html/features/pymol.html b/help/help/html/features/pymol.html
index 2c5c7ad..7bf5651 100644 (file)
--- 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
@@ -221,11 +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