parameter suffix suffix2 rseed set dir = /data/elgar/francis/celegans5073/garant/run1 set dir2 = /data/elgar/francis/celegans5073/garant/run1/{$suffix} set dir3 = /data/elgar/francis/celegans5073/garant/run1/{$suffix2} # Input data set atomlist = celegans5073 set sequence = celegans5073 set cbpl = hncacb # peak lists hncacb set hsqcpl = hs15n set hncapl = hnca set hncocapl = hncoca set hncopl = hnco set cconhpl = cconh set hncacopl = hncaco #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_{$suffix2} set refcbpl = hncacb_{$suffix2} set refhncacopl = hncaco_{$suffix2} # macro to be used for writing out best assignment set savemacro = write1 set name = {$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 = 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 $dir3/$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 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 okHA HA criteria comment on okHA criteria fragment correct okCA CA criteria comment on okCA criteria fragment correct okHB HB criteria comment on okHB criteria fragment correct okCB CB criteria comment on okCB #criteria fragment correct okCD CD #criteria comment on okCD #criteria fragment correct okCG CG #criteria comment on okCG #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