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
http://www.euroscreen.com http://www.euroscreen.com
This message contains information that may be confidential and privileged and is intended solely for the use of the intended recipient. Unless you are the intended recipient (or authorized to receive for the intended recipient), you may not use, copy or disclose to anyone the message and any attachments or any information contained in the message. If you have received this message in error, please notify Euroscreen at +32 71 348 500 or by reply e-mail and destroy all copies of this message and any attachments.