Gnuplot is a freely available plotting utility.
The following (normalmodeplot.gnu) is an example gnuplot script that can be
used to generate graphs of the first three normal modes for a specific system.
This script would be in a directory that contained the directories of the
individual systems (4 plots are being generated with this one script
as-written), which are then accessed individually in the plot command.
The individual .dat files are the ones that were created using
NMWiz and ProDy.
The number of residues should be changed in the set xrange [0:500] line to
reflect the number of residues of the protein, and the set x2tics line should
have “DNA” 400 reflect the residue number where DNA actually begins
(if there is any; otherwise delete it or comment it out).
set encoding iso_8859_1
set term postscript eps enhanced color font "Helvetica, 20";
unset ytics
set xlabel "Residue Number"
set ylabel "PCA Square Fluctuations"
set xrange [1:500]
set xtics border nomirror out
set x2tics border nomirror out rotate by 25 ("DNA" 400)
set boxwidth 0.25
set style fill solid
set output "WT_protein_system_modes.eps";
plot "WT-system/WT-system_mode1.dat" u 1:2 w boxes t "Mode 1" lw 3, \
"WT-system/WT-system_mode2.dat" u 1:2 w boxes t "Mode 2" lw 3, \
"WT-system/WT-system_mode3.dat" u 1:2 w boxes t "Mode 3" lw 3;
set output "MUT-A-system_modes.eps";
plot "MUT-A-system/MUT-A-system_mode1.dat" u 1:2 w boxes t "Mode 1" lw 3, \
"MUT-A-system/MUT-A-system_mode2.dat" u 1:2 w boxes t "Mode 2" lw 3, \
"MUT-A-system/MUT-A-system_mode3.dat" u 1:2 w boxes t "Mode 3" lw 3;
set output "MUT-B-system_modes.eps";
plot "MUT-B-system/MUT-B-system_mode1.dat" u 1:2 w boxes t "Mode 1" lw 3, \
"MUT-B-system/MUT-B-system_mode2.dat" u 1:2 w boxes t "Mode 2" lw 3, \
"MUT-B-system/MUT-B-system_mode3.dat" u 1:2 w boxes t "Mode 3" lw 3;
set output "MUT-C-system_modes.eps";
plot "MUT-C-system/MUT-C-system_mode1.dat" u 1:2 w boxes t "Mode 1" lw 3, \
"MUT-C-system/MUT-C-system_mode2.dat" u 1:2 w boxes t "Mode 2" lw 3, \
"MUT-C-system/MUT-C-system_mode3.dat" u 1:2 w boxes t "Mode 3" lw 3;