parameter suffix rseed

set dir      = /data/barber/lytle/at3g01050/garant
set dir2     = /data/barber/lytle/at3g01050/garant/{$suffix}

# Input data
set atomlist = at3g01050
set sequence = at3g01050
set cbpl         = hncacb1_edit2 	# peak lists hncacb
set hsqcpl       = hs15n2
set hncapl       = hnca
set hncocapl     = hncoca
set hncopl       = hnco2_edit
set cconhpl      = cconh1_spscan
set hncacopl     = hncaco1
set hnca_ass     = hnca_ass
set hncoca_ass   = hncoca_ass
set cconh_ass    = cconh2_ass
set n15noesypl   = n15no_spscan
#set n15tocsypl   = n15to1_spscan3
#set c13noesypl   = c13no_man_unfold
set hcchpl       = hcch2_unfold

#set refhsqcpl       = ass_hs15n_{$suffix2}
#set refhncapl       = hnca_{$suffix2}
#set refhncocapl     = ass_hncoca_{$suffix2}
#set refhncopl       = hnco_fpnew_{$suffix2}
#set refcconhpl      = cconh_fpnew_{$suffix2}
#set refcbpl         = hncacb_fpnew_{$suffix2}
#set refhncacopl      = hncaco_fp_{$suffix2}
#set refn15noesypl   = n15no_spscan_{$suffix2}
#set refn15tocsypl   = to15n_man_{$suffix2}
#set refc13noesypl   = c13no_man_unfold_{$suffix2}
#set refhcchpl       = hcch2_unfold_{$suffix2}

# macro to be used for writing out best assignment
set savemacro   = write9

set name     = {$suffix}
set sizePop  = 100

seed random numbers $rseed

#N15H1
#   set N15H1_w1         = 2
#   set N15H1_w2         = 1
#   set N15H1_acc_w1     = 0.02
#   set N15H1_acc_w2     = 0.2
#   load peaks N15H1 $dir/$hsqcpl   

HNCA
#   set HNCA_acc_w1      = 0.04
#   set HNCA_acc_w2      = 0.15
#   set HNCA_acc_w3      = 0.05
   set HNCA_w1          = 1
   set HNCA_w2          = 3
   set HNCA_w3          = 2
   load peaks HNCA      $dir/$hncapl

HN_CO_CA
#    set HN_CO_CA_acc_w1  = 0.02
#    set HN_CO_CA_acc_w2  = 0.2
#    set HN_CO_CA_acc_w3  = 0.2
    set HN_CO_CA_w1      = 1
    set HN_CO_CA_w2      = 3
    set HN_CO_CA_w3      = 2
    load peaks HN_CO_CA  $dir/$hncocapl

HNCO
#    set HNCO_acc_w1      = 0.04
#    set HNCO_acc_w2      = 0.15
#    set HNCO_acc_w3      = 0.05
    set HNCO_w1          = 1
    set HNCO_w2          = 3
    set HNCO_w3          = 2
    load peaks HNCO      $dir/$hncopl

CBCANH
   set CBCANH_w1     = 1	# w1 of XEASY-list -> w1 (garant) == HN
   set CBCANH_w2     = 3	# w3 of XEASY-list -> w2 (garant) == N
   set CBCANH_w3     = 2	# w2 of XEASY-list -> w3 (garant) == CA/CB
#   set CBCANH_acc_w1 = 0.04	# 
#   set CBCANH_acc_w2 = 0.12
#   set CBCANH_acc_w3 = 0.20
   load peaks CBCANH $dir/$cbpl

C_CO_NH
#    set C_CO_NH_acc_w1   = 0.04
#    set C_CO_NH_acc_w2   = 0.12
#    set C_CO_NH_acc_w3   = 0.2
    set C_CO_NH_w1       = 1
    set C_CO_NH_w2       = 3
    set C_CO_NH_w3       = 2
    load peaks C_CO_NH   $dir/$cconhpl

HN_CA_CO
    set HN_CA_CO_acc_w1   = 0.025
    set HN_CA_CO_acc_w2   = 0.3
    set HN_CA_CO_acc_w3   = 0.3
    set HN_CA_CO_w1       = 1
    set HN_CA_CO_w2       = 3
    set HN_CA_CO_w3       = 2
    load peaks HN_CA_CO   $dir/$hncacopl

N15NOESY 
  set N15NOESY_w1     = 2    # N15 axis
  set N15NOESY_w2     = 3
  set N15NOESY_w3     = 1	
  set N15NOESY_acc_w1 = 0.3
  set N15NOESY_acc_w2 = 0.05
  set N15NOESY_acc_w3 = 0.05
  load peaks N15NOESY $dir/$n15noesypl
  set N15NOESY_imp    = 10.0    # importance of NOESY peaks

#N15TOCSY
#  set N15TOCSY_w1     = 2    # N15 axis
#  set N15TOCSY_w2     = 3
#  set N15TOCSY_w3     = 1	
#  set N15TOCSY_acc_w1 = 0.3
#  set N15TOCSY_acc_w2 = 0.05
#  set N15TOCSY_acc_w3 = 0.05
#  load peaks N15TOCSY $dir/$n15tocsypl

#C13NOESY
#   set C13NOESY_acc_w1 = 0.3
#   set C13NOESY_acc_w2 = 0.025
#   set C13NOESY_acc_w3 = 0.025
#   set C13NOESY_w1     = 2
#   set C13NOESY_w2     = 3
#   set C13NOESY_w3     = 1
#   load peaks C13NOESY $dir/$c13noesypl

HCCH7
   set HCCH7_w1     = 3
   set HCCH7_w2     = 2
   set HCCH7_w3     = 1
   set HCCH7_acc_w1 = 0.3
   set HCCH7_acc_w2 = 0.05
   set HCCH7_acc_w3 = 0.05
   load peaks HCCH7 $dir/$hcchpl

#define peak importance "N15NOESY: * * *" 0.1  
#define peak importance "N15NOESY: N(+0) HN(+0) H(-1)" 1.5
#define peak importance "N15NOESY: N(+0) HN(+0) HN(+1)" 3.0
#define peak importance "N15NOESY: N(+0) HN(+0) HN(-1)" 3.0
#define peak importance "N15NOESY: N(+0) HN(+0) HA(-1)" 3.0
#define peak importance "N15NOESY: N(+0) HN(+0) HA(+0)" 3.0

set pick_acc      = 1.0 #sets maximal difference between chemical shifts of the same atom in different spectra

load sequence $dir/$sequence
#load comparison sequence  $dir/$sequence 

#pseudocorrection #corrections applied when generating expected NOEs from homologous protein

#define atom probability "HE(GLN)" 1.0   # exclude NH2 side chains
#define atom probability "HD(ASN)" 1.0   # exclude NH2 side chains
#define atom probability "HE(ARG)" 1.0   # exclude NH side chains
#define atom probability "NZ(LYS)" 1.0   # exclude NH side chains
#define atom probability "CD(GLN)" 1.0   # exclude NH2 side chains
#define atom probability "CG(ASN)" 1.0   # exclude NH2 side chains
#define atom probability "CD(GLU)" 1.0   # exclude NH2 side chains
#define atom probability "CG(ASP)" 1.0   # exclude NH2 side chains

make coherences			# generate all possible coherences
make couplings			# generate couplings
make noe			# generate noe's if no homologous structure
make peaks			# generate expected peaks

# define shifts according to secondary structure
#define secondary shifts $dir/CalcSecondarytrunc.txt

#load comparison assignments N15NOESY $dir3/$refn15noesypl $dir/$atomlist 0.0
#load comparison assignments N15TOCSY $dir3/$refn15tocsypl $dir/$atomlist 0.0
#load comparison assignments HCCH7 $dir3/$refhcchpl $dir/$atomlist 0.0
#load comparison assignments C13NOESY $dir3/$refc13noesypl $dir/$atomlist 0.0
#load comparison assignments HNCO $dir3/$refhncopl $dir/$atomlist 0.0
#load comparison assignments HNCA $dir3/$refhncapl $dir/$atomlist 0.0
#load comparison assignments HN_CO_CA $dir3/$refhncocapl $dir/$atomlist 0.0
#load comparison assignments CBCANH $dir3/$refcbpl $dir/$atomlist 0.0
#load comparison assignments C_CO_NH $dir3/$refcconhpl $dir/$atomlist 0.0
#load comparison assignments HN_CA_CO $dir3/$refhncacopl $dir/$atomlist 0.0

load assignments HNCA $dir/$hnca_ass $dir/$atomlist 0.0
load assignments HN_CO_CA $dir/$hncoca_ass $dir/$atomlist 0.0
#load assignments HNCO $dir/$hnco_ass $dir/$atomlist 0.0
load assignments C_CO_NH $dir/$cconh_ass $dir/$atomlist 0.0

check inconsistencies

reset user assignments HNCA
#reset user assignments HNCO
reset user assignments HN_CO_CA
#reset user assignments CBCANH
reset user assignments C_CO_NH

# insert here fixed assignments
do i 20 52
   fix assignments "HN($i)"
   fix assignments "N($i)"
#   fix assignments "C($i)"
   fix assignments "CA($i)"
   fix assignments "CB($i)"
   fix assignments "CG($i)"
   fix assignments "CD($i)"
end do

do i 54 108
   fix assignments "HN($i)"
   fix assignments "N($i)"
#   fix assignments "C($i)"   
   fix assignments "CA($i)"
   fix assignments "CB($i)"
   fix assignments "CG($i)"
   fix assignments "CD($i)"
end do

do i 113 115
   fix assignments "HN($i)"
   fix assignments "N($i)"
#   fix assignments "C($i)"   
   fix assignments "CA($i)"
   fix assignments "CB($i)"
   fix assignments "CG($i)"
   fix assignments "CD($i)"
end do

criteria fragment intrainter intra 0 0
criteria fragment intrainter seq 1 1
criteria fragment correct ok
criteria comment on ok
criteria fragment correct okN N
criteria comment on okN
criteria fragment correct okHN HN
criteria comment on okHN
#criteria fragment correct okCA CA
#criteria comment on okCA
criteria fragment correct okHA HA
criteria comment on okHA
criteria fragment correct okHB HB
criteria comment on okHB
#criteria fragment correct okCB CB
#criteria comment on okCB
#criteria fragment correct okC C
#criteria comment on okC
#criteria fragment SScorrect SSok
#criteria comment on SSok
criteria fragment mapping map
criteria comment on map
criteria comment on intra
criteria threshold intra 0.6 0.8
#criteria coherence mapping mapco
#criteria comment on mapco

opt $sizePop $savemacro

quit