/usr/share/ghemical/3.0.0/user-docs/ribbon.html is in ghemical 3.0.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<link href="documentation.css" rel="stylesheet" type="text/css">
<title>Ghemical User Documentation: Objects: Ribbon model</title>
</head>
<body>
<h1>2.1.14 Ribbon model</h1>
<p>Ghemical can produce a ribbon model of a polypeptide. In this model, a ribbon is drawn
along the polypeptide backbone of the protein, parallel to the peptide plane. Ghemical will
detect the secondary structure of the protein and colour the ribbon accordingly:</p>
<ul>
<li>Beta strand - green</li>
<li>Loops - blue</li>
<li>Alpha helix - red</li>
</ul>
<p>The width of the ribbon is increased in helicies and strands. Typically, you will change
the rendering of the molecule to Nothing using the ribbon model so that you can see the
ribbon without the interference from ball-and-stick model of the protein. It is also much faster
to view and change the perspective of the ribbon model, rather than the fully rendered
protein. It can take a considerable length of time make a ribbon object of a large protein.</p>
<H2>Example</H2>
<p>This is a ribbon model of Cytochrome P450 3A4 (CYP3A4) generated in ghemical,
based on the consensus structure modeled by Szklarz and Halpert
<a href="references.html#r_szklarz_halpert_1997">(Szklarz and Halpert, 1997).</A></p>
<img src="images/ribbon.png" width="414" height="431" alt="Screenshot of ribbon model of CYP3A4.">
<hr> <br>
<a href="index.html">Return to index</a> <br>
</body>
</html>
|