JAL-3103 updated help doc to remove default browser choice

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

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 58b06db..25d59bf 100755 (executable)
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -50,7 +50,7 @@
     </li>
     <li>The <a href="#connections"><strong>&quot;Connections&quot;</strong>
         Preferences</a> tab allows you to configure Jalview's internet
-      settings and specify your default web browser.
+      settings.
     </li>
     <li>The <a href="#links"><strong>&quot;Links&quot;</strong>
         Preferences</a> tab shows the currently configured <em>URL
@@ -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
@@ -421,6 +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