X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=0cd6168475804038b778b44eb3e0c7a094bc131e;hb=e502a7571bf01a0354ce8205948dd7a3cda1603b;hp=9a2d2bf851c791f5ad7b3f372b99785183432b15;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html
index 9a2d2bf..0cd6168 100644
--- a/help/html/features/jmol.html
+++ b/help/html/features/jmol.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -32,12 +32,12 @@
     structures opened by entries in the <strong>&quot;Structure&quot;</strong>
     submenu in the <a href="../menus/popupMenu.html">sequence id
       pop-up menu</a> (if you can't see this, then you need to <a
-      href="viewingpdbs.html"
-    >associate a PDB structure</a> with the sequence). Jmol is available
-    from the Jalview desktop and should also run in the JalviewLite
-    applet, providing the browser supports Java 1.5. If Jmol is not
-    available, then the original <a href="pdbviewer.html">internal
-      pdb viewer</a> will be used as a fallback.
+      href="viewingpdbs.html">associate a PDB structure</a> with
+    the sequence). Jmol is available from the Jalview desktop and should
+    also run in the JalviewLite applet, providing the browser supports
+    Java 1.5. If Jmol is not available, then the original <a
+      href="pdbviewer.html">internal pdb viewer</a> will be used as a
+    fallback.
   </p>
   <!-- <p>The following menu entries are provided for viewing structure data<br>
   <ul>
@@ -74,15 +74,18 @@
       based structure superposition was added in Jalview 2.6</em>
   </p>
   <p>
-    <strong>Controls</strong><br> The structure is by default
-    rendered as a ribbon diagram. Moving the mouse over the structure
-    brings up tooltips giving the residue name, PDB residue number and
-    chain code, atom name and number
-    ([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a
-    residue in any associated sequences, then this will be highlighted
-    in each one's alignment window. The converse also occurs - moving
-    the mouse over an associated residue in an alignment window
-    highlights the associated atoms in the displayed structures.
+    <strong>Controls</strong><br> The structure is by default rendered
+    as a ribbon diagram. Moving the mouse over the structure brings up
+    tooltips giving the residue name, PDB residue number and chain code,
+    atom name and number ([RES]Num:Chain.AtomName#AtomNumber). If a
+    mapping exists to a residue in any associated sequences, then this
+    will be highlighted in each one's alignment window. The converse
+    also occurs - moving the mouse over an associated residue in an
+    alignment window highlights the associated atoms in the displayed
+    structures. Press B or use
+    <em>Select&#8594;Select Highlighted columns</em> from any linked
+    alignment window to mark the columns highlighted after mousing over
+    the structure.
   </p>
   <p>Selecting a residue highlights its associated sequence residue
     and alpha carbon location. Double clicking an atom allows distances
@@ -195,7 +198,7 @@
         </strong><em> Colours each residue in the structure with the colour
             of its corresponding residue in the associated sequence as
             rendered in the associated alignment views, including any
-            Uniprot sequence features or region colourings.<br />Pick
+            UniProt sequence features or region colourings.<br />Pick
             which of the associated alignment views are used to colour
             the structures using the <strong>View&#8594;Colour
               by ..</strong> sub menu.
@@ -218,8 +221,8 @@
             colourschemes.<br>
         </strong><em>The remaining entries apply the colourschemes available
             from the standard and user defined <a
-            href="../colourSchemes/index.html"
-          >amino acid colours</a>.
+            href="../colourSchemes/index.html">amino acid
+              colours</a>.
         </em></li>
       </ul></li>
     <li><strong>Jmol<br>
@@ -259,11 +262,10 @@
     Jmol scripting console.</p>
   <p>
     The state of each Jmol display is stored within <a
-      href="jalarchive.html"
-    >Jalview archives</a> as a Jmol state recovery script file. This means
-    that any Jmol visualization effects that you add beyond those
-    provided by Jalview will be able to be stored and recovered along
-    with the displayed alignments in Jalview.
+      href="jalarchive.html">Jalview archives</a> as a Jmol state
+    recovery script file. This means that any Jmol visualization effects
+    that you add beyond those provided by Jalview will be able to be
+    stored and recovered along with the displayed alignments in Jalview.
   </p>
   <p>
     <strong>More Information</strong>
@@ -272,8 +274,8 @@
     Jmol is a sophisticated program in its own right, with its own
     command console and scripting language. Only the essentials have
     been described here - the interested reader is referred to <a
-      href="http://jmol.sourceforge.net/docs/"
-    >Jmol's own comprehensive online documentation</a>.
+      href="http://jmol.sourceforge.net/docs/">Jmol's own
+      comprehensive online documentation</a>.
   </p>
   </p>
 </body>
