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<html>
<head>
<title>
Lesson 5
</title>
</head>
<h1 align=center>
Garlic Tutorial
</h1>
<h2 align=center>
Lesson 5 - How to Select Atoms
</h2>
<hr size="3">
In this lesson, you will learn how to select atoms. The command select (or
whatever command plays this role) is one of the most important commands in
every molecular visualization program.
<br><br>
For this lesson, you will need a true protein structure, not just a single
amino acid as in previous lessons.
<br><br>
Step 1 - obtain the protein structure:
<br><br>
<font color=RED>
Use you web browser to access
<a href="http://www.rcsb.org/pdb">
The Protein Data Bank (www.rcsb.org)
</a>
.
<br>
Type 1HUC into the small search field. Start the search and wait
for the answer.
<br>
Choose the option "Download/Display File".
<br>
Finally, choose file format "PDB", compression "none" in the section
"Download the Structure File" and wait.
<br><br>
</font>
Step 2 - start garlic (if necessary):
<br><br>
<font color=RED>
garlic
<br><br>
</font>
Step 3 - load the structure. You should have the file 1HUC.pdb somewhere
in the path searched by garlic (if you defined the environment variable
MOL_PATH), or in your current working directory.
<br><br>
<font color=RED>
loa 1HUC.pdb
<br><br>
</font>
Step 4 - draw backbone, to simplify the picture:
<br><br>
<font color=RED>
bac
<br><br>
</font>
Step 5 - use different colors for different chains:
<br><br>
<font color=RED>
col chain
<br><br>
</font>
Step 6 - select chain A, draw balls and sticks and change color scheme to CPK:
<br><br>
<font color=RED>
sel a/*/*/*
<br>
bac off
<br>
bon 4
<br>
ato bal
<br>
col cpk
<br><br>
</font>
Step 7 - redefine the internal system origin (the rotation center) and
move chain A to the screen center:
<br><br>
<font color=RED>
cen
<br>
pos 0 0 0
<br><br>
</font>
Step 8 - restrict the selection to aliphatic amino acids and change color
to yellow (chain A):
<br><br>
<font color=RED>
res ali
<br>
col yellow
<br><br>
</font>
Step 9 - select all, make it visible, show only backbone but reduce
the backbone thickness:
<br><br>
<font color=RED>
sel *
<br>
sho
<br>
bac 3
<br><br>
</font>
Step 10 - hide side chains:
<br><br>
Step 10 - select cysteine residues, but only for chains A and C;
make them visible, use spacefill style:
<br><br>
<font color=RED>
sel a,c/*/cys/*
<br>
show
<br>
ato spa
<br><br>
</font>
Step 11 - discard loaded structure:
<br><br>
<font color=RED>
dis all
<br><br>
</font>
<hr size="3">
</html>
|
