cat << EOF > cpar6.cya

info   := normal
name   := par6
tf_type	:= 2
cut_tf := 1000.0
seed   := 35621
cut_upl := 0.1

cyanalib
#dyanalib

read seq ./par6.seq
read prot ./par6.prot
atom shift check
read peaks ./c13no_ed_cyana.peaks assigned integrated
peak set volume=abs(volume)
#caliba 
caliba bb=8.0E+06 dmax=5.5 
write upl c13no_cal.upl
distance delete

#read prot ./n15no_fcp.prot
#atom shift check
read peaks ./n15no_ed_cyana.peaks assigned integrated
peak set volume=abs(volume)
#caliba 
caliba bb=1.9E+07 dmax=5.5
write upl n15no_cal.upl
distance delete

#read prot ./n15no_fcp.prot
#atom shift check
read peaks ./c13no_ar_cyana.peaks assigned integrated
peak set volume=abs(volume)
#caliba
caliba bb=1.5E+06 dmax=5.5
write upl c13no_ar_cal.upl
distance delete

read upl c13no_cal.upl
read upl n15no_cal.upl append
read upl c13no_ar_cal.upl append
distance modify
distance check
write upl par6.upl
#read upl cycle7.upl

read aco par6.aco

#distance select all
distance stat
#dcostat ctmoc_dco
#seqplot ctmoc_seq

nproc=4
calc_all 100 command=anneal steps=10000
overview structures=20 range=158..178,195..251 cor full

cut_upl := 0.3
structures select 1..20
structure violate structures=10 delete=100
write upl par6_viol.upl
write aco par6_viol.aco
 
calc_all 100 command=anneal steps=10000
cut_upl := 0.1
overview file=par6_viol structures=20 range=158..178,195..251 full
ramachandran file=rama_viol nobackground label

EOF

cyana << cpar6.cya > cpar6.out
cpar6
quit


