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JAL-1603 if Chimera selected in Preferences, warn if not installed/found
[jalview.git] / help / html / features / chimera.html
diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index e866597..dbaad73 100644 (file)
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -24,7 +24,7 @@
 </head>
 <body>
 <p><strong>The Chimera Viewer</strong></p>
-<p>Since Jalview 2.8.2, <a href="https://www.cgl.ucsf.edu/chimera/">Chimera</a>
+<p>Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a> (http://www.cgl.ucsf.edu/chimera/)
 has been integrated into Jalview for interactively viewing 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
@@ -69,7 +69,8 @@ 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>
-<p>Basic screen operations (see <a href="https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera help</a> for full details).
+<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">
        <tr>
                <td><strong>Action</strong></td>
@@ -133,6 +134,8 @@ atoms in the displayed structures. For comprehensive details of Chimera's comman
                they are insertions (relative to the associated sequence in the
                alignment) and grey if they are N or C terminal flanks outside the
                region mapped to the alignment window's sequence.</em></li>
+               <li><strong>By Chain<br>
+               </strong><em>Uses the Chimera 'rainbow chain' command to apply a different colour to each chain.</em></li>
                <li><strong>Charge &amp; Cysteine<br>
                </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
                Glutamic Acid) residues in red, and cationic (Lysine or Arginine)