[modeller_usage] modeller usage

[Guido Leoni <>]

Hi, I'm a new modeller use and

    I am trying to use the modeller8v1version on my windows machine to model my protein. but it keeps giving me this following error. Though all the script file, alignment files and pdb files are in the same directory as specified in the script file.

TypeError: 'tuple' object has only read-only attributes <assign to .starting_model>.

My script is:

# Homology modelling by the automodel class

from modeller.automodel import *

log.verbose()

env = environ()

env.io.atom_files_directory = 'C:\Documents and Settings\Zio Charlie\Desktop\PROVE MODELLER2',

a = automodel(env,

alnfile = 'ali4.aln', # alignment filename

knowns = ('1EW2_A', '1K7H_A', '1ED9_A'),

sequence = 'gi|14521248|ref|NP_126723.1|'),

a.starting_model = 1

a.ending_model = 1

a.make()

and my alignment file is:

>P1;gi|14521248|ref|NP_126723.1|

sequence:gi|14521248|ref|NP_126723.1|:1 :

--MMKMKLARFLLIFIIFSSMFP----------FANASPSGVRNVIILIG

DGMGFSQLQLTKLVYGHLN-----------MEDFPYTGIELTDSLSGEVT

DSAAAGTAIATGVKTYNRMISTTNVTGKLVNLTT---------LLEIAQM

LGKATGLVTTTRITHATPAVFASHVPDR-------------------DME

EEIARQLILHNVTVLMGGGREKFS-----------EEVLKLAEDYGYSIV

YTREDLEKVKDG-------------------------KVLGLFAEGHLPY

VLDR-SEEDVSLLEMTKKAIEILEKNPNGFFLMIEGGRIDHACHANDVAS

IVAETKEFDDVVGYVLDYARRRGDTLVIVLADHETGGLGIGLNYGHSVDI

DSIRRIDASIEEMSKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNST

NKYALGNIIGEIISKKLGVGFVSHKHTGEPVPLLAYGPGAENFVGFKHHV

DTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTGDYRVDERDAYATLMLLL

GDLVDTELENIADMDNNGIIDLLDVMAILQASS*

>P1;1ED9_A

structure:pdb_file:1ED9:1 :

TPEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIG

DGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVT

DSAASATAWSTGVKTYNGALGVDIHEKDHPT------------ILEMAKA

AGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGK

GSITEQLLNARADVTLGGGAKTFAET-ATAGEWQGKTLREQAQARGYQLV

SDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCT

PNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCG

QIGETVDLDEAVQRALEFAKKEGNTLVIVTADHA-----------HASQI

VAPDTKAP---GLTQALNTKDGAVMVMSYGNSE-----------------

--------------------EDSQEHTGSQLRIAAYGPHAANVVGLTDQT

DLFYTMKAALGLK-------------------------------------

---------------------------------*

>P1;1EW2_A

structure:pdb_file:1EW2:1 :

--IIPVEEENPDFWNREAAEALG-------AAKKLQPAQTAAKNLIIFLG

DGMGVSTVTAARILKGQKKDKLG-PEIPLAMDRFPYVALSKTYNVDKHVP

DSGATATAYLCGVKGNFQTIGLSAAARFNQCNTTRGNEVIS--VMNRAKK

AGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVPASARQ-EGCQDIA

TQLISN---MDIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLDGKNLV

QEWLAKRQ--------GARYVWNRTELMQASLDPSVTHLMGLFEPGDMKY

EIHRDSTLDPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRAYR

ALTETIMFDDAIERAGQLTSEE-DTLSLVTADHS-----------HVFSF

GGYPLRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLK-DGARPDVTESE

SGSPE-------YRQQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQT

FIAHVMAFAACLEP-YTACDLAPPAGTTDAAHPGRSVVP----ALLPLLA

GTLLLLETATAP---------------------*

>P1;1K7H_A

structure:pdb_file:1K7H:1 :

-------EEDKAYWNKDAQDALD-------KQLGIKLREKQAKNVIFFLG

DGMSLSTVTAARIYKGGLTGKFE-REK-ISWEEFDFAALSKTYNTDKQVT

DSAASATAYLTGVKTNQGVIGLDANTVRTNCSYQLDESLFTYSIAHWFQE

AGRSTGVVTSTRVTHATPAGTYAHVADRDWENDSDVVHDREDPEICDDIA

EQLVFREPGKNFKVIMGGGRRGFF----PEEALDIEDGIPGEREDGKHLI

TDWLDDKASQGA----TASYVWNRDDLLAVDIAN-TDYLMGLFSYTHLDT

VLTRDAEMDPTLPEMTKVAIEMLTKDENGFFLLVEGGRIDHMHHANQIRQ

SLAETLDMEEAVSMALSMTDPE-ETIILVTADHG-----------HTLTI

TGYADRNTDILDFAGISDLDDRRYTILDYGSGPGYHITEDGKRYEPTEED

LKDIN-------FRYASAAPKHSATHDGTDVGIWVNGPFAHLFTGVYEEN

YIPHALAYAACVGTGRTFCD------------------------------

---------------------------------*

Can some one suggest a solution?

 

   Thanks

Guido