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|
<html>
<head>
<title>
Lesson 7
</title>
</head>
<h1 align=center>
Garlic Tutorial
</h1>
<h2 align=center>
Lesson 7 - Draw Helical Wheel
</h2>
<hr size="3">
In this lesson, you will learn how to prepare the helical wheel plot. This
plot may be used to identify amphipatic segments in a protein sequence, i.e.
the amphipatic helices. In this lesson, the solved structure will be used
for demonstration. For more details, read
<a href="../commands/whe.html">
this
</a>
(WHEEL command description).
<br><br>
You can use any protein structure for this lesson. In this example 1HUC.pdb is
used, though you can use any 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. You should have your PDB file (here 1HUC.pdb)
somewhere in the search path (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 3 - select all atoms except hetero atoms. If this is not done the
hetero "residues" (i.e., solvent molecules) will corrupt the helical
wheel plot. The trick is to select hetero residues, and then to select
complement. You don't have to hide hetero residues, so you can skip
the command hide.
<br><br>
<font color=RED>
sel het
<br>
hide
<br>
sel com
<br><br>
</font>
Step 4 - check the number of chains in human cathepsin B. If there are two
or more chains, the residue serial number should not be used as unique
residue identifier.
<br><br>
<font color=RED>
color chain
<br><br>
</font>
Step 5 - there are obviously four chains. Hide all chains except B.
Hide everything, after that select only the chain B and make it visible.
Hetero residues will not be included into selection, so the step 3 was in
fact unnecessary.
<br><br>
<font color=RED>
sel all
<br>
hide
<br>
sel b/*/*/*
<br>
show
<br><br>
</font>
Step 6 - try to find one helix at the chain B surface. Helices may
be easily recognized if using backbone representation of the protein.
It is also practical to use the geometric center of the chain B as the
rotation center, and to move it to the screen center.
<br><br>
<font color=RED>
bac
<br>
cen
<br>
pos 0 0 0
<br><br>
</font>
Step 7 - play with the chain B to find this helix:
<br>
<table border=0 cellspacing=2 cellpading=0>
<td align="center">
76
</td>
<td align="center">
77
</td>
<td align="center">
78
</td>
<td align="center">
79
</td>
<td align="center">
80
</td>
<td align="center">
81
</td>
<td align="center">
82
</td>
<td align="center">
83
</td>
<td align="center">
84
</td>
<td align="center">
85
</td>
<td align="center">
86
</td>
<tr>
<td align="center">
PRO
</td>
<td align="center">
ALA
</td>
<td align="center">
GLU
</td>
<td align="center">
ALA
</td>
<td align="center">
TRP
</td>
<td align="center">
ASN
</td>
<td align="center">
PHE
</td>
<td align="center">
TRP
</td>
<td align="center">
THR
</td>
<td align="center">
ARG
</td>
<td align="center">
LYS
</td>
</table>
<br>
Step 8 - copy the sequence of the chain B to the main sequence buffer.
Note that the helical wheel plot uses the sequence which is stored in the
main sequence buffer. Right now this buffer is empty!
<br><br>
<font color=RED>
seq from 1
<br><br>
</font>
Step 9 - draw helical wheel for residues from 76 to 86:
<br><br>
<font color=RED>
wheel 76-86
<br><br>
</font>
Step 10 - return to the main drawing mode. Hit the escape key or type the
following command:
<br><br>
<font color=RED>
whe off
<br><br>
</font>
Step 11 - discard loaded structure:
<br><br>
<font color=RED>
dis all
<br><br>
</font>
Step 12 - clear the main sequence buffer:
<br><br>
<font color=RED>
seq reset
<br><br>
</font>
<hr size="3">
Do not forget that for helical wheel plot, the main sequence buffer should
be initialized!
<hr size="3">
</html>
|
