Hi, The alignment file should contain: structureX for templates and SequenceX for the target. Why started from model 3:starting_model= 3? hope this help, Yours, Riadh HAMMAMI PhD Student University of Tunis El Manar, TUNISIA »»»»»
Your script is:
from modeller.automodel import * # Load the automodel class
log.verbose()
# Override the 'select_atoms' routine in the 'automodel' class class mymodel(automodel): def select_atoms(self): self.pick_atoms (selection_segment=('923:','924:','925:','926:','927:','928:','929:','930:','931:','932:','933:','934:','935:','936:','937:','938:','939:','940:','941:','942:','943:','944:','945:','946:','947:','948:','949:','950:','951:','952:','953:','954:','955:','956:','957:','958:','959:','960:','961:','962:','963:','964:','965:','966:','967:','968:','969:','970:','971:','972:','973:','974:','975:','976:','977:','978:','979:','980:','981:','982:','983:','984:','985:','986:','987:','988:','989:','990:'), selection_search='segment', pick_atoms_set=1, res_types='all', atom_types='all', selection_from='all', selection_status='initialize')
env = environ() # directories for input atom files env.io.atom_files_directory = 'C:\master' # selected atoms do not feel the neighborhood env.edat.nonbonded_sel_atoms = 2
a = mymodel(env, alnfile = 'fosfalcapirstrano1daq.ali', # alignment filename knowns = '1DAQB', # codes of the templates sequence = '14521248') # code of the target
a.starting_model= 3 # index of the first model a.ending_model = 3 # index of the last model # (determines how many models to calculate) a.make() # do homology modelling ----------------------------------------------------------------------------------------------------------------- Your alignment file should be : >P1;1K7H structurex:1K7H :1 :A : :B :unknown:unknown:-1:-1 ---------------EEDKAYWNKDAQDALDKQLGI---KLREKQAKNVIFFLGDGMSLSTVTAARIYKGGLTGK -FEREKI-SWEEFDFAALSKTYNTD------KQVTDSAASATAYLTGVKTNQGVIGLDANTVRTNCSYQLDESLF TYSIAHWFQEAGRSTGVVTSTRVTHATPAGTYAHVADRDWENDSDVVHDRE--DPE-I--CDDIAEQLVFREPGK NFKVIMGGGRRGFFPEEALDIEDG----IPGERED-----GKHLITDWLDDKASQGATASYVWNRDDLLAV-DIA NTD----YLMGLFSYTHLDTVL---------------------TRDAEMDPTLPEMTKVAIEMLTKDENGFFLLV EGGRIDHMHHANQIRQSLAETLDMEEAVSMALSMT-DPEETIILVTADHGHTLTITGYA------------DRNT DILDFAGISDLDDRRYTILDYGSGPGYHITEDGKRYEPTEEDLKDINFRYASAAPKHSATHDGTDVGIWVNGPFA HLFTGVYEENYIPHALAYAACVGTGRTFCD--------------------------------------------- ------------------------/---------------EEDKAYWNKDAQDALDKQLGI---KLREKQAKNVI FFLGDGMSLSTVTAARIYKGGLTGK-FEREKI-SWEEFDFAALSKTYNTD------KQVTDSAASATAYLTGVKT NQGVIGLDANTVRTNCSYQLDESLFTYSIAHWFQEAGRSTGVVTSTRVTHATPAGTYAHVADRDWENDSDVVHDR E--DPE-I--CDDIAEQLVFREPGKNFKVIMGGGRRGFFPEEALDIEDG----IPGERED-----GKHLITDWLD DKASQGATASYVWNRDDLLAV-DIANTD----YLMGLFSYTHLDTVL---------------------TRDAEMD PTLPEMTKVAIEMLTKDENGFFLLVEGGRIDHMHHANQIRQSLAETLDMEEAVSMALSMT-DPEETIILVTADHG HTLTITGYA------------DRNTDILDFAGISDLDDRRYTILDYGSGPGYHITEDGKRYEPTEEDLKDINFRY ASAAPKHSATHDGTDVGIWVNGPFAHLFTGVYEENYIPHALAYAACVGTGRTFCD* >P1;1EW2 structurex:1EW2 :1 :A : :B :unknown:unknown:-1:-1 ----------IIPVEEENPDFWNREAAEALGAAKKL---QPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKKDK LGPEIPL-AMDRFPYVALSKTYNVD------KHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQCNTTR--GNE VISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVP--AS--ARQEG--CQDIATQLISNM--- DIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLD-----GKNLVQEWLAKR----QGARYVWNRTELMQASLDP SVT----HLMGLFEPGDMKYEI---------------------HRDSTLDPSLMEMTEAALRLLSRNPRGFFLFV EGGRIDHGHHESRAYRALTETIMFDDAIERAGQLT-SEEDTLSLVTADHSHVFSFGGYP------------LRGS SIFGLAPGKARDRKAYTVLLYGNGPGYVLK-DGARPDVTESESGSPEYRQQSAVPLDEETHAGEDVAVFARGPQA HLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP------------------------------------------ -------------------------/----------IIPVEEENPDFWNREAAEALGAAKKL---QPAQTAAKNL IIFLGDGMGVSTVTAARILKGQKKDKLGPEIPL-AMDRFPYVALSKTYNVD------KHVPDSGATATAYLCGVK GNFQTIGLSAAARFNQCNTTR--GNEVISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVP-- AS--ARQEG--CQDIATQLISNM---DIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLD-----GKNLVQEWL AKR----QGARYVWNRTELMQASLDPSVT----HLMGLFEPGDMKYEI---------------------HRDSTL DPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLT-SEEDTLSLVTADH SHVFSFGGYP------------LRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLK-DGARPDVTESESGSPEYR QQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP* >P1;1ED9 structure:1ED9 :1 :A : :B :unknown:unknown:-1:-1 TPEMPVLENRAAQGDITAPGGA--RRLTGD--QTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAE----- -GAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHE------------KD HPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALE-KGGKGSITEQLLN----A RADVTLGGGAKTFA-----------------ETATAGEWQGKTLREQAQARG------YQLVSDAASLNSV-T-- -EANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQV EGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGA VM---------------VMSYGN------------------------------SEEDSQEHTGSQLRIAAYGPHA ANVVGLTDQTDLFYTMKAALGLK---------------------------------------------------- ------------------------/TPEMPVLENRAAQGDITAPGGA--RRLTGD--QTAALRDSLSDKPAKNII LLIGDGMGDSEITAARNYAE------GAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKT YNGALGVDIHE------------KDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKC PGNALE-KGGKGSITEQLLN----ARADVTLGGGAKTFA-----------------ETATAGEWQGKTLREQAQA RG------YQLVSDAASLNSV-T---EANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSV PTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHA HASQIVAPDTKAPGLTQALNTKDGAVM---------------VMSYGN--------------------------- ---SEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK* >P1;1DAQA structurex:1DAQA :1 :A :57 : :unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------MSTKLYGDVNDDGKVNSTDAVALKRYVLRSGISIN TDN-ADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG-------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------* >P1;1DAQB structurex:1DAQB :1 :A :57 : :unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ------------------------/--------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------------------------------MSTKLYGDVND DGKVNSTDAVALKRYVLRSGISINTDN-ADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG*
>P1;14521248 sequenceX:14521248:1 :A : :B :unknown:unknown:-1:-1 ----------------MMKMKLARFLLIFIIFSSMFPFANASPSGVRNVIILIGDGMGFSQLQLTKLVYGHLNME DFPYTGIELTDSLS-----------------GEVTDSAAAGTAIATGVKTYNRMISTTNVTGKL---------VN LTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPDRDMEEEIARQLILHNVT--------------------- ---VLMGGGREKFSEEVLKLAEDYGY---------------------------------SIVYTREDLEKVKDG- -------KVLGLFAEGHLPYVL----------------------DRSEEDVSLLEMTKKAIEILEKNPNGFFLMI EGGRIDHACHANDVASIVAETKEFDDVVGYVLDYARRRGDTLVIVLADHETGGLGIGLNYGHSVDIDSIRRIDAS IEEMSKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNIIGEIISKKLGVGFVSHKHTGEPVPLL AYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTGDYRVDERDAYATLMLLLGDLVDTELE NIADMDNNGIIDLLDVMAILQASS/-----------------MMKMKLARFLLIFIIFSSMFPFANASPSGVRNV IILIGDGMGFSQLQLTKLVYGHLNMEDFPYTGIELTDSLS-----------------GEVTDSAAAGTAIATGVK TYNRMISTTNVTGKL---------VNLTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPDRDMEEEIARQLI LHNVT------------------------VLMGGGREKFSEEVLKLAEDYGY----------------------- ----------SIVYTREDLEKVKDG--------KVLGLFAEGHLPYVL----------------------DRSEE DVSLLEMTKKAIEILEKNPNGFFLMIEGGRIDHACHANDVASIVAETKEFDDVVGYVLDYARRRGDTLVIVLADH ETGGLGIGLNYGHSVDIDSIRRIDASIEEMSKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNI IGEIISKKLGVGFVSHKHTGEPVPLLAYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTG DYRVDERDAYATLMLLLGDLVDTELENIADMDNNGIIDLLDVMAILQASS* _________________________________________________________________________________________