Sophie

Sophie

distrib > Mandriva > cooker > i586 > by-pkgid > eede1088262777189a3d3f16cb3dc560 > files > 293

garlic-1.6-6.i586.rpm

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<head>
<title>
Lesson 3
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<h1 align=center>

Garlic Tutorial

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<h2 align=center>

Lesson 3 - Playing with Two Structures

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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).
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Step 1 - start garlic (if necessary):
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<font color=RED>

garlic
<br><br>

</font>


Step 2 - load trypthophan:
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<font color=RED>

loa trp.pdb
<br><br>

</font>


Step 3 - change TRP color to blue:
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<font color=RED>

col blue
<br><br>

</font>


Step 4 - load phenylalanine:
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<font color=RED>

loa phe.pdb
<br><br>

</font>


Step 5 - change PHE color to red:
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<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:
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<font color=RED>

cat 1
<br>
pos -5 0 0 
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</font>


Step 7 - move phenylalanine to the right:
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<font color=RED>

cat 2
<br>
pos 5 0 0
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</font>


Step 8 etc. - use the command cat (catch) to rotate structures one by one:
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<font color=RED>

Use cat 1 and cat 2 to catch and rotate structures, one by one.
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Translate both structures to the position where they will be overlapped, but
do not use keyword pos!
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</font>


When finished, discard loaded structures:
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<font color=RED>

dis all

</font>

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