phipsigen.README

                    INSTRUCTIONS FOR USE 

Follow the command line usage message. phipsigen -help gives you
the usage message. -gnuplot sets the output for gnuplot (and will
also write the corresponding gnuplot scripts to load easily into
gnuplot. -origin sets the output for origin. -nobin prevents the
script from binning the phi-psi angles.  You will get two sets of
data from this script: prefix.residue.dat which you can plot in 2-D
to get the individual points on the ramachandran torus projection,
and prefix.bin.dat which are the binned data files that plot prob-
abilities as a function of PHI (x) and PSI (y) angles. These are
the files plotted by the gnuplot scripts written by this script.



Command line usage:

phipsigen.py -i <inputfile> -o <output_prefix> -p <prmtop> -y <mdcrd1> <mdcrd2> ... <mdcrdN> {-nobin} -gnuplot (DEFAULT) || -origin

Input file format:
"""
You are allowed any comment line that does not have an equal sign
residue = 4, 5, 8, 20-25, 9
bins = 50x50
"""

residue and bin keywords are case-INsensitive, and must be on different lines. There can be any kind of whitespace you want
separating entries, but the residue lists must be comma-delimited and there must be an x separating the two bin dimensions.
Note that this is the number of bins for PHI x PSI, not the bin width.