parameter suffix suffix2 rseed

set dir      = /data/barber/lytle/at3g01050/garant
set dir2     = /data/barber/lytle/at3g01050/garant/{$suffix}
set dir3     = /data/barber/lytle/at3g01050/garant/{$suffix2}

# Input data
set atomlist = at3g01050
set sequence = at3g01050
set cbpl         = hncacb1_edit 	# peak lists hncacb
set hsqcpl       = hs15n2
set hncapl       = hnca1_edit
set hncocapl     = hncoca2_edit
set hncopl       = hnco2_edit
set cconhpl      = cconh2_spscan
set hncacopl     = hncaco1
#set n15noesypl   = no15n_na_new.peaks~	# peak lists n15noesy
#set c13noesypl   = c13no2_na_new
set hcchpl       = hcch2_unfold

set refhsqcpl       = hs15n2_{$suffix2}
set refhncapl       = hnca1_2a_edit_{$suffix2}
set refhncocapl     = hncoca2_edit_{$suffix2}
set refhncopl       = hnco2_{$suffix2}
set refcconhpl      = cconh2_spscan_{$suffix2}
set refcbpl         = hncacb1_edit_{$suffix2}
set refhncacopl     = hncaco1_{$suffix2}
set refhcchpl       = hcch2_unfold_{suffix2}

# macro to be used for writing out best assignment
set savemacro   = write5

set name     = {$suffix}
set sizePop  = 70

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     = 3    # N15 axis
#  set N15NOESY_w2     = 2
#  set N15NOESY_w3     = 1	
#  set N15NOESY_acc_w1 = 0.12
#  set N15NOESY_acc_w2 = 0.04
#  set N15NOESY_acc_w3 = 0.05
#  load peaks N15NOESY $dir/$n15noesypl
#  set N15NOESY_imp    = 10.0    # importance of NOESY peaks

#C13NOESY
#   set C13NOESY_acc_w1 = 0.3
#   set C13NOESY_acc_w2 = 0.025
#   set C13NOESY_acc_w3 = 0.025
#   set C13NOESY_w1     = 3
#   set C13NOESY_w2     = 1
#   set C13NOESY_w3     = 2
#   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 N15H1 $dir/$refhsqcpl $dir/$atomlist 0.0
load comparison assignments HNCA $dir3/$refhncapl $dir/$atomlist 0.0
load comparison assignments HNCO $dir3/$refhncopl $dir/$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 comparison assignments HCCH7 $dir3/$refhcchpl $dir/$atomlist 0.0
#load comparison assignments N15NOESY $dir3/$refn15noesypl $dir/$atomlist 0.0
#load comparison assignments N15TOCSY $dir3/$refn15tocsypl $dir/$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


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 okHA HA
criteria comment on okHA
criteria fragment correct okHB HB
criteria comment on okHB
criteria fragment correct okCA CA
criteria comment on okCA
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