From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 4 Mar 2022 16:38:01 +0000 (+0000)
Subject: JAL-3746 structure mapping preference docs for JAL-3817
X-Git-Tag: Release_2_11_2_1~29
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8f49a4f326a9a7b0de97682eb62402f66d469cf3;p=jalview.git

JAL-3746 structure mapping preference docs for JAL-3817
---

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index d091272..a33a076 100755
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -236,6 +236,13 @@
     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