#============================================================#
#               test reading 2nd structure                   #
#                                                            #
# show topology.                                             #
#============================================================#

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

# open pdb file
#--------------
database open name = db1  format = pdb  file = ../data/neck_xform.pdb


# read molecule
#--------------
molecule read  name = m1   database = db1  


# create a helix domain
#----------------------
domain create helix = C
domain helix backbone color = [ 1 0 0 ] width = 1 show

# show contact
#-------------
#domain helix contact cutoff = 0.5 atom_names = { CA } show


# create cam domain
#-------------------
domain create d1 = ABD
domain d1 backbone color = [ 1 1 0 ] width = 1 show

# show contact
#-------------
domain d1 contact cutoff = 0.1 use_sidechains = true   use_radii = true
#domain d1 contact cutoff = 1.0 use_sidechains = true 
#domain d1 contact cutoff = 0.5 atom_names = { CA } show


#graphics background color = [ 1 1 1 ]