#============================================================*
#               test domain fitting                          *
#============================================================*

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

# read molecule
molecule read  name = m1   database = neck

# create a some domains
#----------------------
domain create iq1 = AC[760-788]
domain iq1 backbone color = [ 1 0 0 ] width = 2 show

domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0 1 0 ] width = 2 show

domain create iq3 = DC[814-836]
domain iq3 backbone color = [ 0 0 1 ] width = 2 show

domain create hc = C


# output all chains
#------------------ 
domains write atoms list = { iq1 }  file = t1.pdb


# output chain A  only
#--------------------- 
domains write atoms list = { iq1 }  chains = { A } file = t2.pdb
domains write atoms list = { iq1 }  chains = { A[148] } file = t3.pdb
domains write atoms list = { iq1 }  chains = { A[148]=D } file = t4.pdb
domains write atoms list = { iq1 }  chains = { A[148]=D[1] } file = t5.pdb


# output chain A only and change chain id to D
#--------------------------------------------- 
domains write atoms list = { iq1 }  chains = { A=D } file = t6.pdb
domains write atoms list = { iq1 }  chains = { A=D[20] } file = t7.pdb


# output all chains with different chain ids 
#------------------------------------------- 
domains write atoms list = { iq1 }  chains = { A=D C=E } file = t8.pdb


# output chains with renumbered seq
#---------------------------------- 
domains write atoms list = { iq1 }  chains = { A[10] C=E[20] } file = t9.pdb


# output chains with renumbered seq
#---------------------------------- 
domains write atoms list = { iq1 }  chains = { A[10-20]=D[1] } file = t10.pdb
domains write atoms list = { iq1 }  chains = { A[10-20]=D } file = t11.pdb


# output chains with single chain id
#----------------------------------- 
domains write atoms list = { iq1 }  one_chain = A[10] file = t12.pdb