#============================================================*
#            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_strand.pdb 

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

# create domains 
#---------------
domain create helix = CD
# 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_c = C
domain dna_c backbone color = [ 1 0 0 ] show = true
domain dna_c bonds atoms = false bond_color = element show = true

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



# create cylinder
#----------------
solid create  name = cyl1  type = cylinder  \
              domain = helix                \
              region = CD                   \
              color = [ 1 0 0 ]             \
              display = line                \
              show = true