From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 17 Oct 2023 15:11:15 +0000 (+0100)
Subject: JAL-4090 JAL-4089 document use of selected columns for superposition, and add links... 
X-Git-Tag: Release_2_11_4_0~135^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fdoc%2FJAL-4090_Release_2_11_3_0;p=jalview.git

JAL-4090 JAL-4089 document use of selected columns for superposition, and add links to Pymol for individual viewer capabilities
---

diff --git a/help/help/html/features/viewingpdbs.html b/help/help/html/features/viewingpdbs.html
index 947b96b..df76f89 100755
--- a/help/help/html/features/viewingpdbs.html
+++ b/help/help/html/features/viewingpdbs.html
@@ -87,7 +87,7 @@
     <strong>Structure Viewers in the Jalview Desktop</strong><br /> The
     <a href="jmol.html">Jmol viewer</a> has been included since Jalview
     2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>,
-    provided it is installed and can be launched by Jalview. ChimeraX and PyMOL
+    provided it is installed and can be launched by Jalview. ChimeraX and <a href="pymol.html">PyMOL</a>
     support is included from Jalview 2.11.2. The default
     viewer can be configured in the <a href="preferences.html#structure">Structure
       tab</a> in the <strong>Tools&rarr;Preferences</strong> dialog box.
@@ -114,19 +114,23 @@
     un-tick the <strong>Superpose Structures</strong> checkbox.
 
   </p>
-  <p>
-    <em>Superposing structures</em><br/>Jalview superposes structures using
-    the visible portions of any associated sequence alignments. A
-    message in the structure viewer's status bar will be shown if not
-    enough aligned columns were available to perform a superposition.
-  </p>
-  <p>
-  See the <a href="jmol.html">Jmol
-    </a> and <a href="chimera.html">Chimera</a> help pages for
-      more information about their capabilities.</p>
-  
-
-  <p>
+	<p>
+		<em>Superposing structures</em><br />Jalview superposes structures
+		using the currently selected columns (if more than 3 columns are
+		selected), or the visible portions of any associated sequence
+		alignments. Depending on the viewer, Root Mean Squared Deviation (RMS
+		or RMSD) for each pair of superpositions may be output in the
+		structure viewer's console.
+	</p>
+	<p>A message in the structure viewer's status bar will be shown if
+		not enough aligned columns were available to perform a superposition.
+	</p>
+	<p>
+		See the <a href="jmol.html">Jmol</a>, <a href="chimera.html">Chimera/X</a>
+		and <a href="pymol.html">Pymol</a> help pages for more information
+		about their individual capabilities.
+	</p>
+	<p>
     <strong>Retrieving sequences from the PDB</strong><br>You can
     retrieve sequences from the PDB using the <a
       href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences