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[modeller_usage] model-segment.py problem

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Subject: [modeller_usage] model-segment.py problem
From: Guido Leoni <>
Date: Tue, 11 Oct 2005 15:01:51 +0200

Hi
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
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

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