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
Direct +32 71 348 509
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