# RigiMOL input file.


# load the PDB structures we're going to morph

load

   pdb
      filename morphFrom.pdb
   end   

   pdb 
      filename morphTo.pdb
   end

end

# determine connectivity 

reference

   # how much VDW overlap generally determines a bond
   bond_cutoff    = 0.4

   # how far out are our neighbors?
   neighbor_cutoff = 3.0

   # should we treat HIS, ASN, GLN as symmetric (1=yes, 0=no)
   coarse_symmetry = 1 

end

# generate the difference distance matrix

compare end

# now cluster (the settings rarely need to be changed).

analyze

   group_distance_cutoff     =   0.25  #  Distance (Angstroms)
   group_angle_cutoff        =  30.00  #  Angle (Degrees) 0-180
   group_shape_cutoff        =  25.00  #  Shape Ratio (25-500)

   cluster_distance_cutoff   =   1.25  #  Distance (Angstroms)
   cluster_angle_cutoff      =  75.00  #  Angle (Degrees) 0-180
   cluster_shape_cutoff      = 250.00  #  Shape Ratio (25-500)

   domain_similarity_cutoff  =   1.20  #  Ratio > 1.0
   domain_size_cutoff        =  10     #  Atom Count
   domain_shape_cutoff       = 500.00  #  Shape Ratio (25-500)

end

# fit domains (domain 1 = the largest domain found)
# to turn this off, comment out this block

#fit
#   mode = domain
#   domain = 1
#end

# write out the interpolation

write 

   # write an interpolation PDB file (contains multiple models)

   interpolation
      output = eMovie_rigimol_morph.pdb
      steps = 30
      from 1 to 2
   end

   # write a PyMOL script which colors each domain uniquely and
   # defines browsable selections

   #analysis
   #   domains = rigimol_domains.pml
   #   min_domain_size = 4
   #end

   #write fitting information to standard output for the largest domains

   #fits
   #   max_domains 10
   #end

end

# terminate RigiMOL
   
stop