## GARANT MACROS: ExampleResAss2 - example of resonance assignment with 3D spectra
##
## Example of a resonance assignment using heteronuclear spectra and the structure
## of the protein  

parameter suffix rseed

set dir      = /hlr/nmr/sgi/bartelsc/easy

# set echo = no

# Input data
set atomlist     = cyclo.prot
set sequence     = cyclo.seq
set cbpl         = cbcanh	# peak lists hncacb
set cbcopl       = cbcaco	# peak lists cbca(co)hn
set hbcopl       = hbhaco	# peak lists hbha(co)hn
#set hcacopl      = hcaco	# peak lists hcaco
#set hncopl       = hnco	# peak lists hnco
set hncapl       = hnca		# peak lists hnca
set n15noesypl   = noesy15n     # peak lists noesy15n
set hnca_ass	= ass_hnca
#set hnco_ass	= ass_hnco
set cbcaco_ass	= ass_cbcaco
set cbcanh_ass	= ass_cbcanh

# X-Ray structure
set strucs = $dir/cyclo_H.cor
        # minimal allowed distance
set limitdist  = 2.0
set limitdist2 = 4.0
        # minimal required number of structures with distance < limitdist
set minStrucs  = 1
set minStrucs2 = 1


set savemacro  = writegyr-noe	# macro to be used for writing out best assignment

set name     = em{$suffix}	# suffix to name output files
set sizePop  = 100		# 10      ... for testing
				# 100-200 ... for production

seed random numbers $rseed

CBCANH
   set CBCANH_w1     = 3	# w1 of XEASY-list -> w3 (garant) == CA/CB
   set CBCANH_w2     = 1	# w2 of XEASY-list -> w1 (garant) == Hn
   set CBCANH_w3     = 2	# w3 of XEASY-list -> w2 (garant) == N
   set CBCANH_acc_w1 = 0.06	# accuracy of peak picking in HN-axis
   set CBCANH_acc_w2 = 0.16	# acc. in N-axis
   set CBCANH_acc_w3 = 0.24	# acc. in CA/CB-axis
   load peaks CBCANH $dir/$cbpl

CBCACONH
   set CBCACONH_w1     = 3	# first col. in peaklist -> third axis (garant)
   set CBCACONH_w2     = 1
   set CBCACONH_w3     = 2
   set CBCACONH_acc_w1 = 0.06	# accuracy of peak picking in HN-axis
   set CBCACONH_acc_w2 = 0.16   # acc. in N-axis
   set CBCACONH_acc_w3 = 0.24	# acc. in CA/CB-axis
   set CBCACONH_imp    = 3.0
   load peaks CBCACONH $dir/$cbcopl

HNCA
   set HNCA_w1     = 3
   set HNCA_w2     = 1
   set HNCA_w3     = 2
   set HNCA_acc_w1 = 0.06
   set HNCA_acc_w2 = 0.16
   set HNCA_acc_w3 = 0.24
   set HNCA_imp    = 3.0
   load peaks HNCA $dir/$hncapl

HBHACONH
   set HBHACONH_w1     = 3     # first col. in peaklist -> third axis (garant)
   set HBHACONH_w2     = 1
   set HBHACONH_w3     = 2
   set HBHACONH_acc_w1 = 0.06  # accuracy of peak picking in HN-axis
   set HBHACONH_acc_w2 = 0.16  # acc. in N-axis
   set HBHACONH_acc_w3 = 0.05  # acc. in HA/HB-axix
   set HBHACONH_imp = 2.0       # importance of HBHACONH peaks
   load peaks HBHACONH $dir/$hbcopl

N15NOESY 
   set N15NOESY_w1     = 3     # aliphatic H's
   set N15NOESY_w2     = 2     # HN axis
   set N15NOESY_w3     = 1     # N15 axis
   set N15NOESY_acc_w1 = 0.16
   set N15NOESY_acc_w2 = 0.06
   set N15NOESY_acc_w3 = 0.05
   set N15NOESY_imp    = 1.0    # importance of NOESY peaks
   load peaks N15NOESY $dir/$n15noesypl

set pick_acc      = 1.1		# e.g. HBHACONH_acc_w1 * pick_acc
				# defines chemical shift difference
				# between different spectra

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

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
#load comparison sequence  $dir/$sequence 

make coherences			# generate all possible coherences
make couplings			# generate couplings

pseudocorrection
load coord $strucs
make distance noe floating $minStrucs  $limitdist  1.0
make distance noe floating $minStrucs2 $limitdist2 0.2


make peaks			# generate expected peaks

#list expected peaks "CBCACONH: *(ASN) * *"	# check exclusion of NH2
#list expected peaks "CBCACONH: *(GLN) * *"
#list expected peaks "CBCANH: *(ARG) * *"
#list expected peaks "CBCANH: *(LYS) * *"

				# load assignments for comparison
load comparison assignments HNCA     $dir/$hnca_ass    $dir/$atomlist   0.0
load comparison assignments CBCANH   $dir/$cbcanh_ass  $dir/$atomlist   0.0
load comparison assignments CBCACONH $dir/$cbcaco_ass  $dir/$atomlist   0.0

reset user assignments HNCA
reset user assignments CBCANH
reset user assignments CBCACONH

criteria fragment intrainter intra 0 0
criteria fragment intrainter seq 1 1
criteria comment on intra
criteria threshold intra 0.6 0.8
criteria fragment correct ok
criteria comment on ok
criteria fragment SScorrect SSok
criteria comment on SSok
criteria fragment correct okHN HN
criteria comment on okHN
criteria fragment correct okCA CA
criteria comment on okCA
criteria fragment correct okCB CB
criteria comment on okCB
criteria fragment mapping map
criteria comment on map

opt $sizePop $savemacro

quit