JAL-1668 updated documentation

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

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 31ca419..11b43c8 100644 (file)
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -32,7 +32,7 @@ id pop-up menu</a> (if you can't see this, then you need to <a
 sequence). Chimera is available from the Jalview desktop, provided Chimera has been separately installed.</p>
 <p>You can set a default choice of Jmol or Chimera structure viewer in <a href="preferences.html#structure"> Preferences</a>. 
 You can also optionally specify the path to the Chimera program here (if it differs from the standard paths searched by Jalview).
 sequence). Chimera is available from the Jalview desktop, provided Chimera has been separately installed.</p>
 <p>You can set a default choice of Jmol or Chimera structure viewer in <a href="preferences.html#structure"> Preferences</a>. 
 You can also optionally specify the path to the Chimera program here (if it differs from the standard paths searched by Jalview).

-<p>The following menu entries are provided for viewing structure data<br>
+<!-- <p>The following menu entries are provided for viewing structure data<br>

   <ul>
     <li>The <strong>&quot;Structure&#8594;View
         Structure&#8594;</strong> submenu allows a single PDB structure to be chosen
   <ul>
     <li>The <strong>&quot;Structure&#8594;View
         Structure&#8594;</strong> submenu allows a single PDB structure to be chosen

@@ -49,10 +49,10 @@ You can also optionally specify the path to the Chimera program here (if it diff
       currently selected sequence.<br /></li>
   </ul>
   <br> 
       currently selected sequence.<br /></li>
   </ul>
   <br> 

-</p>
+</p> -->

 <p><a name="align"><strong>Superposing structures based
 on their aligned sequences</strong></a><br>
 <p><a name="align"><strong>Superposing structures based
 on their aligned sequences</strong></a><br>

-<p>If several structures are available on the alignment, you may add
+If several structures are available on the alignment, you may add

 additional structures to an existing Chimera 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
 additional structures to an existing Chimera 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

@@ -63,12 +63,12 @@ menu bar of the structure view window to superpose the structures using
 the updated alignment.<br>
 </p>
 <p><strong>Chimera Controls</strong><br>
 the updated alignment.<br>
 </p>
 <p><strong>Chimera Controls</strong><br>

-<p>The structure is by default rendered as a ribbon diagram. Moving the
+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
 ([RES]Num:Chain). Moving the mouse over an
 associated residue in an alignment window highlights the associated
 mouse over the structure brings up tooltips giving the residue name, PDB
 residue number and chain code
 ([RES]Num:Chain). Moving the mouse over an
 associated residue in an alignment window highlights the associated

-atoms in the displayed structures. For comprehensive details of Chimera's commands, refer to the tool's Help menu.</p>
+atoms in the displayed structures. For comprehensive details of Chimera's commands, refer to the tool's Help menu.

 <p>Basic screen operations (see <a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera help</a> 
 (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html) for full details).
 <table border="1">
 <p>Basic screen operations (see <a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera help</a> 
 (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html) for full details).
 <table border="1">