# This line is a comment.
# For further information on any of the chosen parameters and possible default values, please refer to the documentation.

# Input file(s) of the contact count histogram data obtained with print-coor contact or print-coor aa-contact mode. Providing input data is mandatory.
# For subtraction mode, specify two input files comma-separated. Subtraction will be performed file 1 - file 2. Note that for subtraction, providing orientations is mandatory.
Input = 2pcc_ccp-cc_fe2.dat, 2pcc_ccp-cc_fe3.dat

# Number of total encounter complexes reported in your simulation for normalizing the contact count data.
# Setting this option is mandatory when performing a subtraction of results from two runs.
# For subtraction, specify the two total orientation counts comma separated in the same order as the corresponding input files.
# Orientations can either be provided as MCMap orientation files (structdist.gz) or as numbers.
# If no number of orientations is provided, no normalization will be performed.
Orientations = 828757, 832136

# Name of the plotted histogram output file. Plot will be written as PNG.
Plot = 2pcc_fe2-fe3_difference_plot.png 

# Title for the plot. Title needs to be surrounded by "".
Title = "Difference map for CcP with Cc(Fe2+) - Cc(Fe3+)"

# Label for the x-axis (receptor amino acid/atom), label needs to be surrounded by "".
xlabel = "Amino acid number CcP"

# Label for the y-axis (ligand amino acid/atom), label needs to be surrounded by "".
ylabel = "Amino acid number Cc" 

# Optional switch for plotting count data on a logarithmic scale if using single, non-normalized input.
# Can be True or False.
Logscale = False

# PQRM file of the receptor.
Receptor = yccp.pqrm

# PQRM file of the ligand.
Ligand = ycc.pqrm

# Percentage of residues with top counts (or top and lowest counts for subtraction) with respect to the total number of contacts to be visualized with the PyMOL script.
Display = 0.1

# Output file for a text report on the top contacts that will be visualized on the protein surface and their contact counts.
MaxContacts = report_difference_plot.txt

# Output file for the receptor PyMOL script.
ReceptorPml = yccp_script_difference_map.pml

# Output file for the ligand PyMOL script.
LigandPml = ycc_script_difference_map.pml
