#============================================================*
#            test simulation of cylinders from domain        *
#                                                            *
# allign cylinders with previous one.                        *
#============================================================*

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


# open pdb file
#--------------
database open name =  neck_xform  format = pdb file =  neck_xform.pdb

# read molecule
#--------------
molecule read  database =  neck_xform  name = m1  model = 1  type = protein

# create domains 
#---------------
domain create hc = C
# translate domain so that ground joint will be (0,0,0)
domain hc  xform translation = [ 0.15334 -0.208601 -0.332707 ]
domain hc  backbone  color = [ 1 0 0 ] width = 1 show

domain create hj = C
domain hj  xform translation = [ 3.15334 -0.208601 -0.332707 ]
domain hj  backbone  color = [ 0 1 0 ] width = 1 show

# create cylinders
#-----------------
solid create  name = cyl1  type = cylinder  \
              radius = 0.22                 \
              domain = hc                   \
              region = C[762-780]           \
              atoms = { CA }                \
              color = [ 1 1 1 ]             \
              display = solid               \
              show = true