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<html>
<head>
<title>
Lesson 12
</title>
</head>
<h1 align=center>
Garlic Tutorial
</h1>
<h2 align=center>
Lesson 12 - Replace Selected Residues
</h2>
<hr size="3">
In this lesson you will learn how to replace selected residues. The
structure used in this example will be 1HUC.pdb, but you can use any other
protein structure.
<br><br>
Before starting with this lesson, read something about the command
<a href="../commands/rep.html">
REPLACE
</a>
.
<br><br>
Step 1 - start garlic (if not started already):
<br><br>
<font color=RED>
garlic
<br><br>
</font>
Step 2 - load the structure:
<br><br>
<font color=RED>
load 1HUC.pdb
<br><br>
</font>
Step 3 - change color:
<br><br>
<font color=RED>
color cold
<br><br>
</font>
Step 4 - select the residue 26 in the chain A:
<br><br>
<font color=RED>
sel a/26/*/*
<br><br>
</font>
Step 5 - define the replacement for this residue:
<br><br>
<font color=RED>
seq = ser
<br><br>
</font>
Step 6 - replace CYS 26 by SER:
<br><br>
<font color=RED>
replace
<br><br>
</font>
Move the residue 26 closer to check the replacement (use numeric keys).
<br><br>
Step 7 - discard structure:
<br><br>
<font color=RED>
dis all
<br><br>
</font>
<hr size="3">
</html>
|
