#    File Names:
monomer input/1oel_A.pdb
monomer_ms input/1oel_A.pdb.ms
log-file multifit.log
prot_lib /viola1/home/kerenl/bioinformatics/projects/multifit/data/chem.lib

#   Symmetry Parameters:
#    symmetry_params <symmetry_of (trimer=3, tetramer=4, etc)>
symmetry_params 7

#    Scoring Parameters:
#        scoreParams <small_interfaces_ratio> <max_penetration> <ns_thr> <w1 w2 w3 w4 w5>
#    <small_interfaces_ratio> - the ratio of the low scoring transforms to be removed
#    <max_penetration> - maximal allowed penetration between molecules surfaces
#    <ns_thr> - normal score threshold
#    <w1 w2 w3 w4 w5> - scoring weights for ranges:
#                [-5.0,-3.6],[-3.6,-2.2],[-2.2,-1.0],[-1.0,1.0],[1.0-up]
scoreParams 0.1 -5.0 0.5 -8 -4 0 1 0

#    Density Parameters:
density input/groel-11.5A.mrc
density_resolution 11.5
#######   Advanced Parameters
#    Clustering Parameters:
#    clusterParams < axis_angle_thr DEGREES > < min_cluster_size > < distance_between_centers_of_mass >
clusterParams 18 1 2.0

#    Base Parameters:
#    baseParams <min_base_dist> <max_base_dist>
baseParams 5.0 50.0

#    Grid Parameters:
#      grid <grid_step> <max_distance> <vol_func_radius>
grid 0.5 6.0 6.0

#    Surface Parameters:

# surfacePruneThereshold - threshold fore surface pruning, i.e. no 2 points with distanca below this thr are left  for matching
surfacePruneThereshold 1.5