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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
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<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
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>"Structure→View
Structure→</strong> submenu allows a single PDB structure to be chosen
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>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
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
-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).
+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">
<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)
git://source.jalview.org / jalview.git / blobdiff