Hello,

I have a problem with MODELLER8v2.

Traceback (most recent call last):

File "TASSERvsGPR43.py", line 15, in ?

a.make()

File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\loopmodel.py", l

ine 28, in make

automodel.make(self, exit_stage)

File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\automodel.py", l

ine 100, in make

self.homcsr(exit_stage)

File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\automodel.py", l

ine 318, in homcsr

aln = self.read_alignment()

File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\automodel.py", l

ine 312, in read_alignment

aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence])

File "M:\People\LPetain\Modeller8v2\modlib\modeller\alignment.py", line 36, in

append

return self.__int_append('alignment.append', io, libs, vars)

File "M:\People\LPetain\Modeller8v2\modlib\modeller\alignment.py", line 68, in

__int_append

libs=libs.modpt, **vars)

File "M:\People\LPetain\Modeller8v2\modlib\modeller\util\top.py", line 33, in

read_alignment

return _modeller.read_alignment(aln, io, libs, *args)

_modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found

in the alignment file; ALIGN_CODES( 1) = tasser

I have seen in the same problem in the problem list (http://salilab.org/archives/modeller_usage/2006/msg00162.html)

But I don't understand this problem since my script is:

from modeller.automodel import *

log.verbose()

env=environ()

class myloop(loopmodel):

def select_loop_atoms(self):

self.pick_atoms(selection_segment=('145:','173:'),selection_status='INITIALIZE')

a=myloop(env,alnfile='TASSER_GPR43.ali',knowns='tasser', sequence='GPR43')

a.starting_model=1

a.ending_model=1

a.md_level=None

a.loop.strating_model=1

a.loop.ending_model=5

a.loop.md_level=refine.fast

a.make()

and it must be correct.

Coulp you please help me?

Thanks by advance.

Ludovic PETAIN

Trainee in Chemoinformatics

EUROSCREEN SA

Tel +32 71 348 500

Fax +32 71 348 519

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