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<html>
<head>
<title>
Lesson 3
</title>
</head>
<h1 align=center>
Garlic Tutorial
</h1>
<h2 align=center>
Lesson 3 - Playing with Two Structures
</h2>
<hr size="3">
In this lesson, you will learn how to work with two or more structures.
The original source package contains two PDB files: trp.pdb and phe.pdb.
Each contains a single amino acid: trp.pdb = tryptophan,
phe.pdb = phenylalanine. In this lesson, tryptophan will be colored blue,
while phenylalanine will be colored red. Note the role of the command
cat (catch).
<br><br>
Step 1 - start garlic (if necessary):
<br><br>
<font color=RED>
garlic
<br><br>
</font>
Step 2 - load trypthophan:
<br><br>
<font color=RED>
loa trp.pdb
<br><br>
</font>
Step 3 - change TRP color to blue:
<br><br>
<font color=RED>
col blue
<br><br>
</font>
Step 4 - load phenylalanine:
<br><br>
<font color=RED>
loa phe.pdb
<br><br>
</font>
Step 5 - change PHE color to red:
<br><br>
<font color=RED>
col red
<br><br>
</font>
Two structures will be distinguished by color and by the identifier:
tryptophan is treated as structure number 1, and phenylalanine is treated
as structure number 2. Two structures are now overlapping.
<br>
Step 6 - move tryptophan to the left:
<br><br>
<font color=RED>
cat 1
<br>
pos -5 0 0
<br><br>
</font>
Step 7 - move phenylalanine to the right:
<br><br>
<font color=RED>
cat 2
<br>
pos 5 0 0
<br><br>
</font>
Step 8 etc. - use the command cat (catch) to rotate structures one by one:
<br><br>
<font color=RED>
Use cat 1 and cat 2 to catch and rotate structures, one by one.
<br>
Translate both structures to the position where they will be overlapped, but
do not use keyword pos!
<br><br>
</font>
When finished, discard loaded structures:
<br><br>
<font color=RED>
dis all
</font>
<hr size="3">
</html>
|
