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<head>
<title>
PLO, PLOT
</title>
</head>
<h1 align=center>
PLO, PLOT
</h1>
<hr size="3">
<font color=#880000>
<b>
NAME
<br>
</b>
</font>
PLO, PLOT - draw hydrophobicity function(s).
<br><br>
<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>
PLO HYD
<br>
PLO HYD start_index end_index
<br>
PLO WEI
<br>
PLO WEI start_index end_index
<br>
PLO MOM
<br>
PLO MOM start_index end_index
<br>
PLO SID
<br>
PLO SID start_index end_index
<br>
PLO F1
<br>
PLO F2
<br>
PLO F3
<br>
PLO F4
<br>
PLO F5
<br>
PLO F6
<br>
PLO F7
<br>
PLO OFF
<br>
PLOT HYDROPHOBICITY
<br>
PLOT HYDROPHOBICITY start_index end_index
<br>
PLOT WEIGHTED
<br>
PLOT WEIGHTED start_index end_index
<br>
PLOT MOMENT
<br>
PLOT MOMENT start_index end_index
<br>
PLO SIDED
<br>
PLO SIDED start_index end_index
<br>
PLOT F1
<br>
PLOT F2
<br>
PLOT F3
<br>
PLOT F4
<br>
PLOT F5
<br>
PLOT F6
<br>
PLOT F7
<br>
PLOT OFF
<br><br>
<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>
Draw averaged hydrophobicity, weighted hydrophobicity, hydrophobic moment,
sided hydrophobicity or some other hydrophobicity function. Two or more
keywords may be combined in the same line. All hydrophobicity functions
will be calculated using the sequence from the main sequence buffer,
the current sliding window width (if required) and the current
hydrophobicity scale. To calculate the hydrophobic moment one more
parameter is required: the rotation angle between adjacent residues.
<br><br>
Seven additional hydrophobicity functions may be found in these source files:
<br>
F1: hyphob_function1.c
<br>
F2: hyphob_function2.c
<br>
F3: hyphob_function3.c
<br>
F4: hyphob_function4.c
<br>
F5: hyphob_function5.c
<br>
F6: hyphob_function6.c
<br>
F7: hyphob_function7.c
<br><br>
The averaged hydrophobicity will be shown as red line and the hydrophobic
moment will be shown as blue line. The sided hydrophobicity (on one side and
on another side) will be represented by two lines (magenta and violet).
Weighted hydrophobicity will be colored violet too. The information about
the residue covered by the pointer (mouse) will be visible in the output
window (bottom right corner of the main window), while the sequence
neighborhood of the current residue will be visible above the plot
(top of the main window).
<br><br>
If the entire sequence is used for calculation, there is a chance that plot
will contain the straight line at the end. This portion of the plot refers to
solvent molecules, which are typically stored to the end of PDB file. This
trailing line may be easily removed by adjusting the range of residue numbers.
Here are two examples:
<br><br>
The first image was prepared using all residues from 200 to the last one,
including solvent molecules.
<br><br>
<img src="plot1.gif">
<br><br>
The second image was prepared using residues from 200 to 280, omitting the
solvent molecules.
<br><br>
<img src="plot2.gif">
<br><br>
<font color=#880000>
<b>
KEYWORDS
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
KEYWORD
<br>
(SHORT)
</td>
<td align="left">
KEYWORD
<br>
(LONG)
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
OFF
</td>
<td align="left">
OFF
</td>
<td align="left">
Return to the main drawing mode (draw atomic coordinates).
<br>
Instead using this command, you can hit the ESCAPE key.
</td>
<tr>
<td align="left">
HYD
</td>
<td align="left">
HYDROPHOBICITY
</td>
<td align="left">
Draw averaged hydrophobicity.
</td>
<tr>
<td align="left">
WEI
</td>
<td align="left">
WEIGHTED
</td>
<td align="left">
Draw weighted hydrophobicity.
</td>
<tr>
<td align="left">
MOM
</td>
<td align="left">
MOMENT
</td>
<td align="left">
Draw hydrophobic moment.
</td>
<tr>
<td align="left">
SID
</td>
<td align="left">
SIDED
</td>
<td align="left">
Draw sided hydrophobicity for both sides (two lines).
</td>
<tr>
<td align="left">
F1
</td>
<td align="left">
F1
</td>
<td align="left">
Draw hydrophobicity function F1 (hyphob_function1.c).
</td>
<tr>
<td align="left">
F2
</td>
<td align="left">
F2
</td>
<td align="left">
Draw hydrophobicity function F2 (hyphob_function2.c).
</td>
<tr>
<td align="left">
F3
</td>
<td align="left">
F3
</td>
<td align="left">
Draw hydrophobicity function F3 (hyphob_function3.c).
</td>
<tr>
<td align="left">
F4
</td>
<td align="left">
F4
</td>
<td align="left">
Draw hydrophobicity function F4 (hyphob_function4.c).
</td>
<tr>
<td align="left">
F5
</td>
<td align="left">
F5
</td>
<td align="left">
Draw hydrophobicity function F5 (hyphob_function5.c).
</td>
<tr>
<td align="left">
F6
</td>
<td align="left">
F6
</td>
<td align="left">
Draw hydrophobicity function F6 (hyphob_function6.c).
</td>
<tr>
<td align="left">
F7
</td>
<td align="left">
F7
</td>
<td align="left">
Draw hydrophobicity function F7 (hyphob_function7.c).
</td>
</table>
<br>
<font color=#880000>
<b>
PARAMETERS
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
PARAMETER
<br>
(SHORT)
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
start_index
</td>
<td align="left">
The actual number of the first residue.
<br>
Note that serial numbers are not used!
</td>
<tr>
<td align="left">
end_index
</td>
<td align="left">
The actual number of the last residue.
</td>
</table>
<br>
<font color=#880000>
<b>
MOUSE USAGE
<br>
</b>
</font>
Mouse may be used to retrieve the information about averaged hydrophobicity
and hydrophobic moment for a given residue. This residue is treated as the
central residue of the current sliding window. The numerical data, along with
residue name and serial number will be visible in the output window (bottom
right corner). The sequence neighborhood of this residue will be visible above
the plot. The information will be associated with the residue which has the
same horizontal position (x coordinate) as the mouse pointer.
<br><br>
<img src="plot3.gif">
<br><br>
<font color=#880000>
<b>
EXAMPLES
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
COMMAND
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
load 2por.pdb
<br>
seq from 1
<br>
scale eis
<br>
win 7
<br>
angle 180
<br>
plot hyd mom 1-300
</td>
<td align="left">
Load porin coordinates, copy sequence to
<br>
the main sequence buffer, select Eisenberg
<br>
hydrophobicity scale, set window width to 7
<br>
and set angle to 180 degrees. Draw averaged
<br>
hydrophobicity and hydrophobic moment for
<br>
residues from 1 to 300.
</td>
<tr>
<td align="left">
seq load sample.fasta
<br>
scale eis
<br>
angle 100
<br>
plot mom
</td>
<td align="left">
Read the file sample.fasta, which contains
<br>
the protein sequence in FASTA format (one
<br>
letter code), select Eisenberg scale, set
<br>
angle to 100 and draw hydrophobic moment.
</td>
<tr>
<td align="left">
plot off
</td>
<td align="left">
Return to default drawing mode.
<br>
Instead using this command, you can hit the ESCAPE key.
</td>
</table>
<br>
<font color=#880000>
<b>
MATHEMATICAL BACKGROUND
<br>
</b>
</font>
Both the averaged hydrophobicity and the hydrophobic moment are calculated
using a rectangular sliding window. If there are N residues in the sliding
window, the averaged hydrophobicity is equal to:
<br>
<img src="plot_eq1.gif">
<br>
Hydrophobic moment is equal to:
<br>
<img src="plot_eq2.gif">
<br>
If you are searching for amphipatic alpha helices, set alpha to 100 degrees.
To identify amphipatic beta strands, use 180 degrees. You can change alpha
by using the command ANGLE.
<br><br>
<font color=#880000>
<b>
NOTES
<br>
</b>
</font>
(1) Instead using the command PLOT OFF, the ESCAPE key may be pressed to
return to the main drawing mode.
<br><br>
(2) PLOT uses only the sequence stored to the main sequence buffer. Read
description of the command SEQ (SEQUENCE) to learn how to initialize this
buffer.
<br><br>
(3) If you plot both the averaged hydrophobicity and the hydrophobic moment,
the output window (bottom right corner) will contain the hydrophobic moment
of the central residue.
<br><br>
(3) Every time you change hydrophobicity scale, don't forget to refresh the
plot (i.e., execute the command PLOT once more).
<br><br>
<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>
SEQUENCE is used to copy, define or load the sequence. ANGLE defines the
rotation angle between adjacent residues. SCALE is used to specify the
hydrophobicity scale. WINDOW is used to set the sliding window width.
<br><br>
<hr size="3">
</html>
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