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
33
34
35
36
37
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<link rel="stylesheet" type="text/css" href="RD.css">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="content-type">
</head>
<body>
<h2>Changing the View</h2>
The software provides a number of options that control the display of
embeddings in PyMol. These are accessible via checkboxes at the top of
the results tree:
<ol>
<li><b>Show Protein?:</b> if this is checked, the protein structure
will be displayed along with each embedding and the reference
molecule.
<li><b>Show Neighborhood?:</b>
when checked, this causes the surface of the protein around the
reference molecule to be displayed.
This option is disabled unless <tt>Show Protein?</tt> is checked.
<li><b>Show H Bonds:</b>
when checked, this causes likely hydrogen bonds between the aligned
embedding and the protein to be drawn.
<li><b>Show Collisions:</b>
when checked, this causes close contacts between the
embedding and the protein to be drawn.
</ol>
</body>
</html>
|
