Hi I have modeller8.1 on a windows machine. I try to use the model-segment.pyscript but modeller send me always the same error: forrtl: severe (64): input conversion error, unit -5, file Internal Fo ad Image PC Routine Line Source libifcoremd.dll 0025DD7A Unknown Unknown Unknown libifcoremd.dll 0025B010 Unknown Unknown Unknown libifcoremd.dll 002261B8 Unknown Unknown Unknown libifcoremd.dll 00226670 Unknown Unknown Unknown libifcoremd.dll 0027F5F9 Unknown Unknown Unknown mod8v1.exe 00494996 Unknown Unknown Unknown mod8v1.exe 00491E53 Unknown Unknown Unknown mod8v1.exe 00474A41 Unknown Unknown Unknown mod8v1.exe 0042D906 Unknown Unknown Unknown mod8v1.exe 00422ED8 Unknown Unknown Unknown python23.dll 26D0A705 Unknown Unknown Unknown python23.dll 26C99DA7 Unknown Unknown Unknown python23.dll 26CAF9E6 Unknown Unknown Unknown python23.dll 26CAC424 Unknown Unknown Unknown python23.dll 26CADAAE Unknown Unknown Unknown python23.dll 26CE8CF0 Unknown Unknown Unknown python23.dll 26C99DA7 Unknown Unknown Unknown python23.dll 26CAF9E6 Unknown Unknown Unknown python23.dll 26CAC424 Unknown Unknown Unknown python23.dll 26CADAAE Unknown Unknown Unknown python23.dll 26CAF4A9 Unknown Unknown Unknown python23.dll 26CAF1F9 Unknown Unknown Unknown python23.dll 26CAC250 Unknown Unknown Unknown python23.dll 26CAF3FD Unknown Unknown Unknown python23.dll 26CAF1F9 Unknown Unknown Unknown python23.dll 26CAC250 Unknown Unknown Unknown python23.dll 26CAF3FD Unknown Unknown Unknown python23.dll 26CAF1F9 Unknown Unknown Unknown python23.dll 26CAC250 Unknown Unknown Unknown python23.dll 26CADAAE Unknown Unknown Unknown python23.dll 26CAF4A9 Unknown Unknown Unknown python23.dll 26CAF1F9 Unknown Unknown Unknown python23.dll 26CAC250 Unknown Unknown Unknown python23.dll 26CADAAE Unknown Unknown Unknown python23.dll 26CA8922 Unknown Unknown Unknown python23.dll 26D22BD4 Unknown Unknown Unknown python23.dll 26D22B86 Unknown Unknown Unknown python23.dll 26D22B50 Unknown Unknown Unknown python23.dll 26D21B2E Unknown Unknown Unknown python23.dll 26D21569 Unknown Unknown Unknown python23.dll 26D214B4 Unknown Unknown Unknown mod8v1.exe 004086BC Unknown Unknown Unknown mod8v1.exe 00401347 Unknown Unknown Unknown mod8v1.exe 005E8C41 Unknown Unknown Unknown mod8v1.exe 005E679B Unknown Unknown Unknown kernel32.dll 7C816D4F Unknown Unknown Unknown _____________________________________________________________ my 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 ----------------------------------------------------------------------------------------------------------------- my alignment file is : >P1;1K7H structure: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 structure: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 structure:1DAQA :1 :A :57 : :unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------MSTKLYGDVNDDGKVNSTDAVALKRYVLRSGISIN TDN-ADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG-------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------* >P1;1DAQB structure:1DAQB :1 :A :57 : :unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ------------------------/--------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------------------------------MSTKLYGDVND DGKVNSTDAVALKRYVLRSGISINTDN-ADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG* >P1;14521248 sequence: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* _________________________________________________________________________________________
someone can help my? thank's in advance
Guido Leoni wrote: > I have modeller8.1 on a windows machine. I try to use the > model-segment.py script but modeller send me always the same error: > forrtl: severe (64): input conversion error, unit -5, file Internal Fo
Assuming your template structure is PDB code 1daq, then you should check your initial generated model, 14521248.ini. You only have template information for a small part of the system, so Modeller can only guess the structure of the rest from the internal coordinates (it generates an extended chain conformation). This gives some of your atoms X coordinates of over 1000 angstroms, which cannot be represented in the PDB format (you'll see ******** instead). This is what is confusing Modeller; it's a limitation of the PDB format.
We will probably switch to using PDBML or MMCIF as the default coordinate output format in future releases of Modeller, which will solve this numbering problem, but even then, without template information, your model will be very poor. You should probably try to find a template to cover other parts of your sequence.
Ben Webb, Modeller Caretaker
participants (2)
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Guido Leoni -
Modeller Caretaker