# PLO, PLOT

NAME
PLO, PLOT - draw averaged hydrophobicity and/or hydrophobic moment.
SYNOPSIS
PLO HYD
PLO HYD start_index end_index
PLO MOM
PLO MOM start_index end_index
PLO SID
PLO SID start_index end_index
PLO OFF
PLOT HYDROPHOBICITY
PLOT HYDROPHOBICITY start_index end_index
PLOT MOMENT
PLOT MOMENT start_index end_index
PLO SIDED
PLO SIDED start_index end_index
PLOT OFF
DESCRIPTION
Draw averaged hydrophobicity hydrophobic moment or sided hydrophobicity. Two or more keywords may be combined in the same line. The averaged hydrophobicity, hydrophobic moment and/or sided hydrophobicity will be calculated using the sequence from the main sequence buffer, the current sliding window width and the current hydrophobicity scale. To calculate the hydrophobic moment one more parameter is required: the rotation angle between adjacent residues.
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). 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).
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:
The first image was prepared using all residues from 200 to the last one, including solvent molecules.
The second image was prepared using residues from 200 to 280, omitting the solvent molecules.
KEYWORDS

KEYWORD (SHORT) | KEYWORD (LONG) | DESCRIPTION
OFF | OFF | Return to the main drawing mode (draw atomic coordinates). Instead using this command, you can hit the ESCAPE key.
HYD | HYDROPHOBICITY | Draw averaged hydrophobicity.
MOM | MOMENT | Draw hydrophobic moment.
SID | SIDED | Draw sided hydrophobicity for both sides (two lines).

PARAMETERS

PARAMETER (SHORT) | DESCRIPTION
start_index | The actual number of the first residue. Note that serial numbers are not used!
end_index | The actual number of the last residue.

MOUSE USAGE
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.
EXAMPLES

COMMAND | DESCRIPTION
load 2por.pdb seq from 1 scale eis win 7 angle 180 plot hyd mom 1-300 | Load porin coordinates, copy sequence to the main sequence buffer, select Eisenberg hydrophobicity scale, set window width to 7 and set angle to 180 degrees. Draw averaged hydrophobicity and hydrophobic moment for residues from 1 to 300.
seq load sample.fasta scale eis angle 100 plot mom | Read the file sample.fasta, which contains the protein sequence in FASTA format (one letter code), select Eisenberg scale, set angle to 100 and draw hydrophobic moment.
plot off | Return to default drawing mode. Instead using this command, you can hit the ESCAPE key.

MATHEMATICAL BACKGROUND
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:
Hydrophobic moment is equal to:
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.
NOTES
(1) Instead using the command PLOT OFF, the ESCAPE key may be pressed to return to the main drawing mode.
(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.
(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.
(3) Every time you change hydrophobicity scale, don't forget to refresh the plot (i.e., execute the command PLOT once more).
RELATED COMMANDS
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.