parameter suffix rseed protein set dir = . # set dir = /data/elgar/cesg/at3g51030/3garant set dir2 = ./{$suffix} #set dir2 = /data/elgar/cesg/at3g51030/3garant/{$suffix} # Input data set atomlist = {$protein} set sequence = {$protein} set cbpl = hncacb # peak lists hncacb set hsqcpl = hs15n set hncapl = hnca set hncocapl = hncoca set hncopl = hnco set cconhpl = cconh #set hcconhpl = hcconh set hncacopl = hncaco #set hncocacbpl = hncocacb #set n15noesypl = no15n_na_new.peaks~ # peak lists n15noesy #set c13noesypl = c13no2_na_new #set hcchpl = hcch_sol_unfold #set refhsqcpl = hs15n_{$suffix2} #set refhncapl = hnca_{$suffix2} #set refhncocapl = hncoca_{$suffix2} #set refhncopl = hnco_{$suffix2} #set refcconhpl = cconh_{$suffix2} #set refhcconhpl = hcconh_{$suffix2} #set refhncocacbpl = hncocacb_{$suffix2} #set refcbpl = hncacb_{$suffix2} #set refhncacopl = hncaco_{$suffix2} # macro to be used for writing out best assignment set savemacro = write set name = {$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 #CBCACONH # set CBCACONH_acc_w1 = 0.02 # set CBCACONH_acc_w2 = 0.2 # set CBCACONH_acc_w3 = 0.2 # set CBCACONH_w1 = 1 # set CBCACONH_w2 = 3 # set CBCACONH_w3 = 2 # load peaks CBCACONH $dir/$hncocacbpl 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 = 0.025 # 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 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 # 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 CBCACONH $dir3/$refhncocacbpl $dir/$atomlist 0.0 #load comparison assignments C_CO_NH $dir3/$refcconhpl $dir/$atomlist 0.0 #load comparison assignments HC_CO_NH $dir3/$refhcconhpl $dir/$atomlist 0.0 #load comparison assignments HN_CA_CO $dir3/$refhncocapl $dir/$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 okHN HN criteria comment on okHN criteria fragment correct okCA CA criteria comment on okCA #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