#============================================================*
#            test simulation of dna using cylinders          *
#============================================================*

# set units
#----------
units
units scale  name = mass   uname = reducedMass   value = 10000.0


# open pdb file
#--------------
database open name = dna  format = pdb  file = dna_bend.pdb 

# read molecule
#--------------
molecule read  database = dna name = m1  model = 1  type = dna 

# create domains 
#---------------
domain create helix = AB
# translate domain so that ground joint will be (0,0,0)
#domain helix xform translation = [ 0.15334 -0.208601 -0.332707 ]
#domain helix backbone color = [ 1 0 0 ] show = true
#domain helix bonds atoms = true  bond_color = element show = true

domain create dna_a = A
domain dna_a backbone color = [ 1 0 0 ] show = true
domain dna_a bonds atoms = false bond_color = element show = true

domain create dna_b = B
domain dna_b backbone color = [ 0 1 0 ] show = true
domain dna_b bonds atoms = false bond_color = element show = true