Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

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

diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html
index 2f10196..ac2489b 100644 (file)
--- a/help/html/features/jmol.html
+++ b/help/html/features/jmol.html
@@ -61,28 +61,25 @@
 </p> -->
   <p>
     <a name="align"><strong>Superposing structures based on
-        their aligned sequences</strong></a><br> If several structures are
-    available on the alignment, you may add additional structures to an
-    existing Jmol view by selecting their entry in the appropriate
-    pop-up menu. Jalview will ask you if you wish to add the structure
-    to the existing alignment, and if you do, it will import and
-    superimpose the new PDB file using the corresponding positions from
-    the alignment. If the alignment is subsequently edited, you can use
-    the <a href="#sAlign"><em>Jmol&#8594;Align</em></a> menu option from
-    the menu bar of the structure view window to superpose the
-    structures using the updated alignment.<br> <em>Sequence
+        their aligned sequences</strong></a><br> If several structures are shown
+    in a view, you can superimpose them using the corresponding
+    positions from the alignment via the <a href="#sAlign"><em>Jmol&#8594;Align</em></a>
+    menu option from the menu bar of the structure view window. <br> <em>Sequence
       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