X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpymol.html;h=7bf565132455311237618eb848d9819b87e2a8d1;hb=17aaf80d4e11248d8cb947b310303a898426092e;hp=573310acc36b6f6283d268659dbc4a4ab2943807;hpb=1a0a6c0b1966cc2025e983a8f92de54af2f90636;p=jalview.git

diff --git a/help/help/html/features/pymol.html b/help/help/html/features/pymol.html
index 573310a..7bf5651 100644
--- 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
-    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 />
@@ -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 corresponging to moused over residues
-      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