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<html>
<head>
<title>
Lesson 9
</title>
</head>
<h1 align=center>
Garlic Tutorial
</h1>
<h2 align=center>
Lesson 9 - Venn Diagram
</h2>
<hr size="3">
In this simple lesson, you will learn how to prepare the Venn diagram with
some residue counts. There is nothing special in this routine and experts
will not find it very useful. It is primarily intended for students and
other newbies, which are interested in the residue composition of the given
protein.
<br><br>
The only information required to prepare the Venn diagram is the protein
sequence. In this example, the sequence will be extracted from PDB data.
Another approach will be to load the sequence from some FASTA file.
The PDB file used here is 1HUC.pdb, but you can replace it with any PDB
file which contains the protein structure.
<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 - discard all hetero atoms:
<br><br>
<font color=RED>
sel het
<br>
sel com
<br><br>
</font>
Step 4 - restrict your selection to chains A and B:
<br><br>
<font color=RED>
res a,b/*/*/*
<br><br>
</font>
Step 5 - extract sequence:
<br><br>
<font color=RED>
seq from 1
<br><br>
</font>
Step 6 - draw Venn diagram with residue counts:
<br><br>
<font color=RED>
venn
<br><br>
</font>
Step 7 - discard the structure:
<br><br>
<font color=RED>
dis all
<br><br>
</font>
Step 8 - clear the sequence buffer. You can omit this command.
<br><br>
<font color=RED>
seq reset
<br><br>
</font>
<hr size="3">
</html>
|
