</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>"Structure"</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
([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>
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 & Cysteine<br>
</strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
Glutamic Acid) residues in red, and cationic (Lysine or Arginine)