X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpreferences.html;h=a33a076396fdb462866dc3623e1fbfe9784db8af;hb=9d2d74b49cd06966eaad8796c87386be1e296057;hp=5fda2dfcbf2ba3abb28758f13d7589eb5725fd61;hpb=28a1247c88a7cc31a836da99a1d795072ca543a7;p=jalview.git

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 5fda2df..a33a076 100755
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -64,6 +64,10 @@
     <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong>
         Preferences</a> tab contains settings affecting behaviour when editing alignments.
     </li>
+    <li>The <a href="#startup"><strong>&quot;Startup&quot;</strong>
+        Preferences</a> tab allows you to adjust how much memory is
+      allocated to Jalview when it is launched.
+    </li>
     <li>The <a href="../webServices/webServicesPrefs.html"><strong>&quot;Web
           Service&quot;</strong> Preferences</a> tab allows you to configure the <a
       href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
@@ -222,17 +226,22 @@
     <em>Add Temperature Factor annotation to alignment</em> - if
     selected, values extracted from the Temperature Factor column for
     the backbone atoms in the PDB file will be extracted as annotation
-    lines shown on the alignment.
+    lines shown on the alignment.<br/><em>Since 2.11.2, scores from the Temperature Column for structures imported via the 3D-Beacons network may be shown instead as model quality or reliability scores.</em>
   <p>
-    <em>Default structure viewer</em> - choose Jmol or CHIMERA for
+    <em>Default structure viewer</em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
     viewing 3D structures.
   <p>
-    <em>Path to Chimera program</em> - Optional, as Jalview will search
-    standard installation paths for Windows, Linux or MacOS. If you have
-    installed Chimera in a non-standard location, you can specify it
-    here, by entering the full path to the Chimera executable program.
-    Double-click this field to open a file chooser dialog.
+    <em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
+    standard installation paths for Windows, Linux or MacOS. If Jalview cannot locate the installation for your selected structure viewer, a dialog will be shown. If you have
+    installed the chosen viewer in a non-standard location, you can specify it
+    here, by entering the full path to its executable.<br/>For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also <em>double-click this field</em> to open a file chooser dialog.</p>
   <p>
+    <em>Sequence &lt;-&gt; Structure Mapping Method</em> - This setting controls whether
+    Jalview attempts to retrieve mappings between Uniprot protein
+    sequences and 3D structures in the PDBe with SIFTS, or constructs a
+    mapping by conservative alignment between the sequences and chains
+    in the 3D structure data using the Needleman and Wunsch algorithm.
+    SIFTS is enabled by default. 
   <p>
     <em>PDB Fields shown in Search and Structure Summaries</em> - ticks
     in this table indicate fields shown by default when browsing results
@@ -249,11 +258,33 @@
     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>
@@ -399,6 +430,17 @@
     loaded onto the alignment will automatically sort the alignment.
   </p>
   <p>&nbsp;</p>
+  <p>
+    <a name="startup"><strong>Startup</strong></a>
+  </p>
+  <p>
+    When Jalview is launched it by default examines the available memory
+    and requests up to 90% to be allocated to the application, or 32G,
+    which ever is smaller. The <em>Startup</em> tab allows you to adjust
+    the maximum percentage and hard limits for Jalview memory allocation
+    stored in your .jalview_properties file.
+  </p>
+  <p>&nbsp;</p>
   <em>Web Services Preferences</em> - documentation for this tab is
   given in the
   <a href="../webServices/webServicesPrefs.html">Web Services