parameter suffix rseed protein 

set dir      = .
set dir2     = ./{$suffix}

# Input data
set atomlist = {$protein}
set sequence = {$protein}
set hsqcpl       = hs15n 	
set hncapl       = hnca
#set hncocapl     = hncoca
set hncopl       = hnco
set cbpl         = hncacb
set cconhpl      = cconh
set hbhaconhpl     = hbhaconh
set hncacopl     = hncaco
#set hcconhpl	 = hcconh
set hcchpl       = hcch_unfold       # must be unfolded
#set n15tocsypl   = to15n
set hncacb_ass     = hncacb_ass
set hncaco_ass   = hncaco_ass
set hnco_ass     = hnco_ass

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

set name     = {$suffix}  #suffix to name output files
set sizePop  = 100         # 10  ...for testing
                          # 25-100 ...for production

seed random numbers $rseed

N15H1
   set N15H1_w1         = 2       # w1 of garant -> w2 of XEASY list == N
   set N15H1_w2         = 1       # w2 of garant -> w1 of XEASY list == HN
#   set N15H1_acc_w1     = 0.02
#   set N15H1_acc_w2     = 0.2
   load peaks N15H1 $dir/$hsqcpl   

HNCA
#   set HNCA_acc_w1      = 0.04   # w1 of garant -> w1 of XEASY list == HN
#   set HNCA_acc_w2      = 0.15   # w2 of garant -> w3 of XEASY list == N
#   set HNCA_acc_w3      = 0.05   # w3 of garant -> w2 of XEASY list == CA
   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

#HC_CO_NH
#    set HC_CO_NH_acc_w1   = 0.025
#    set HC_CO_NH_acc_w2   = 0.3
#    set HC_CO_NH_acc_w3   = 0.02
#    set HC_CO_NH_w1       = 1
#    set HC_CO_NH_w2       = 3
#    set HC_CO_NH_w3       = 2
#    load peaks HC_CO_NH   $dir/$hcconhpl

HBHACONH
   set HBHACONH_acc_w1 = 0.025
   set HBHACONH_acc_w2 = 0.3
   set HBHACONH_acc_w3 = 0.02
   set HBHACONH_w1     = 1
   set HBHACONH_w2     = 3
   set HBHACONH_w3     = 2
   load peaks HBHACONH   $dir/$hbhaconhpl

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

#N15TOCSY
#  set N15TOCSY_w1     = 2    # H axis
#  set N15TOCSY_w2     = 3    # 15N axis
#  set N15TOCSY_w3     = 1    # HN axis	
#  set N15TOCSY_acc_w1 = 0.05
#  set N15TOCSY_acc_w2 = 0.3
#  set N15TOCSY_acc_w3 = 0.05
#  load peaks N15TOCSY $dir/$n15tocsypl

HCCH24
   set HCCH24_w1     = 3
   set HCCH24_w2     = 2
   set HCCH24_w3     = 1
   load peaks HCCH24 $dir/$hcchpl

set pick_acc      = 1.0   #e.g. HNCA_acc_w1 * pick_acc
                          #defines maximal difference between 
                          #chemical shifts in different spectra 

load sequence  $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 CalcSecondarytrunc.txt

load assignments HNCO $dir/$hnco_ass $dir/$atomlist 0.0
load assignments CBCANH $dir/$hncacb_ass $dir/$atomlist 0.0
load assignments HN_CA_CO $dir/$hncaco_ass $dir/$atomlist 0.0

check inconsistencies

#insert fixed assignments here
do i 8 124
   fix assignments "HN($i)"
   fix assignments "N($i)"
   fix assignments "C($i)"
   fix assignments "CA($i)"
   fix assignments "CB($i)"
end do

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

# this section defines the columns listed in the report (.log)
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 okHA HA
criteria comment on okHA
#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