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<html>
<head>
<title>
Lesson 11
</title>
</head>
<h1 align=center>
Garlic Tutorial
</h1>
<h2 align=center>
Lesson 11 - Creating Small Structure
</h2>
<hr size="3">
In this lesson you will learn how to create a short alpha helix. The
structure created using the method described here may be saved as any
other structure.
<br><br>
Before starting with this lesson, read something about the command
<a href="../commands/cre.html">
CREATE
</a>
.
<br><br>
Step 1 - start garlic (if not started already):
<br><br>
<font color=RED>
garlic
<br><br>
</font>
Step 2 - prepare a short sequence (polyalanine, eight residues):
<br><br>
<font color=RED>
seq = ala ala ala ala ala ala ala ala
<br><br>
</font>
Step 3 - initialize the secondary structure (let's play with an alpha helix):
<br><br>
<font color=RED>
str = hhhh hhhh
<br><br>
</font>
Step 4 - create a short alpha helix:
<br><br>
<font color=RED>
create
<br><br>
</font>
Step 5 - save your structure:
<br><br>
<font color=RED>
save test.pdb
<br><br>
</font>
Step 6 - discard the structure:
<br><br>
<font color=RED>
dis all
<br><br>
</font>
That's all!
<br><br>
<hr size="3">
</html>
|
