JAL-3633 Help documentation updated

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 5fda2df..58b06db 100755 (executable)
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -249,11 +249,33 @@
     browser application.
   </p>
   <p>
-    <em>Proxy Server</em><br> If you normally use a proxy server
-    for using the internet, you must tick the box &quot;Use a Proxy
-    Server&quot; and enter the address and port details as necessary.
+    <em>Proxy Server</em><br>
+    There are three settings to choose from:<br>
+    <ul>
+           <li><em>No proxy servers</em> will configure Jalview to use a
+                   direct internet connection.</li>
+           <li><em>System proxy servers</em> will configure Jalview to use
+                   the proxy server passed to it by your system at startup.</li>
+           <li><em>Use these proxy servers:</em> allows you to set a custom
+                   proxy server.</li>
+    </ul>
+    If you normally use a proxy server for using the internet, you must
+    choose one of <em>System proxy servers</em>, or if these have not been
+    passed correctly you should set your own proxy servers to use by selecting
+    <em>Use these proxy servers</em>.
+    You will then need to enter the host and port details as necessary.
     Web Services will not work if you are using a proxy server and do
-    not enter the settings here.
+    not choose the system proxy or enter your own settings here.<br>
+    There are separate host and port settings for HTTP and HTTPS proxies.
+    Often these are the same but you should enter the host and port into both
+    rows.<br>
+    You can also check the <em>Authentication required</em> box if your proxy
+    requires username and password authentication.  You can enter both the
+    <em>Username</em> and <em>Password</em> but only the <em>Username</em> will
+    be stored in Jalview's preferences file, the password will only be stored
+    until the end of the current Jalview session.<br>
+    This means that if the proxy settings are still valid, Jalview will ask for
+    the password when it starts the next session.
   </p>
   <p>
     <em>Usage statistics, Questionnaire and Version checks</em><br>