###########################
# test creating a model   #
###########################

# open pdb file
database open name = neck format = pdb  file = iq.pdb

# read molecule
molecule read  name = m1   database = neck


# create a some domains

domain create iq1 = AC[762-788]
domain iq1 backbone color = [ 1 0 0 ] width = 2 show

domain create iq2 = BC[788-813]
domain iq2 backbone color = [ 0 1 0 ] width = 2 show


# create bodies

body create  name = ground   type = ground
body create  name = 1        type = rigid   domain = iq1
body create  name = 2        type = rigid   domain = iq2


# create joints

joint create            \
      name = 1          \
      type = ball       \
      domain = iq1      \
      res = C762        \
      use = CA

joint 1 color = [ 1 0 0 ] msize = 0.1 shading = color show = true 
joint 1 bodies = { ground 1 }

joint create            \
      name = 2          \
      type = pin        \
      domain = iq1      \
      res = C788        \
      use = CA

joint 2 color = [ 0 1 0 ] msize = 0.1 shading = flat display = line show = true 
joint 2 bodies = { 1 2 }


# create a course-grained model

model create name = model_1

# add joints
model model_1 add joint = 1
model model_1 add joint = 2

# add bodies
model model_1 add rigid body = 1
model model_1 add rigid body = 2
model model_1 add body = ground


model model_1 joints msize = 0.5 show = true

model model_1 bodies msize = 0.5 show = true