Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppre...

[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 5a3fe7a..6708c57 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>
@@ -209,11 +213,6 @@
     structure information read from PDB will be processed and annotation
     added to associated sequences.
   <p>
-    <em>Use RNAView for secondary structure</em> - if selected, the
-    pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
-    will be called to derive secondary structure information for RNA
-    chains.
-  <p>
     <em>Add secondary structure annotation to alignment</em> - if
     selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
       implementation DSSP</a> will be used to add annotation to polypeptide
@@ -224,7 +223,7 @@
     the backbone atoms in the PDB file will be extracted as annotation
     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, CHIMERA, CHIMERAX or PYMOL for
+    <em><strong>Default structure viewer</strong></em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
     viewing 3D structures.
   <p>
     <em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
@@ -232,6 +231,13 @@
     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
     of a free text search via the PDB sequence fetcher, or 3D structures
@@ -419,6 +425,17 @@
     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