X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpymol.html;h=7bf565132455311237618eb848d9819b87e2a8d1;hp=c6a2ae26df3f98a18ae55af6fd314381fe357679;hb=a7634a9f5f5f691a7bff7bb05ca21a340aa2f834;hpb=efba321f20b819819c0b1cd9c9133d9d1a2ab314

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