Dear MODELLER users,
I get this error message " rdpir___648E> Alignment sequence not found in PDB file: 1 ../atom_files\1ba4.pdb " in my log file when I try and run a homology model. When I reduce the number of residues in the sequence to just four the model runs OK. What is wrong, can anyone suggest anything?? I've enclosed my files :screen output, B04_2742_111_002.ali, Loop-005.py and Loop-005.log
And the -v command always gives an error too??
regards and thanks in advance.
Mike
The screen output is:
C:\Program Files\Modeller8v2\examples\automodel>mod8v2 loop-005.py -v
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "loop-005.py", line 24, in ?
a.make() # do the actual homology modelling
File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\loopmodel.py", line 28, in make
automodel.make(self, exit_stage)
File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 100, in make
self.homcsr(exit_stage)
File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 318, in homcsr
aln = self.read_alignment()
File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 312, in read_alignment
aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence])
File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line 36, in append
return self.__int_append('alignment.append', io, libs, vars)
File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line 68, in__int_append
libs=libs.modpt, **vars)
File "C:\Program Files\Modeller8v2\modlib\modeller\util\top.py", line 33, in read_alignment
return _modeller.read_alignment(aln, io, libs, *args)
_modeller.error: rdpir___648E> Alignment sequence not found in PDB file:1 ../atom_files\1ba4.pdb
B04_2742_111_002.ali file
>P1;1ba4
structureX:1ba4:.:.:.:.:
MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRXDTE TEGVPSTAIR EISLLKELNH
PNIVKLLDVI HTENKLYLVF EFLHQDLKKF MDAS------*
>P1;1M8Qb
structureX:1M8Qb:.:.:.:.:
---------- ---------- ---------- ---------- ---------- ----------
---------- ---------- ---------- ----KQPRQY*
>P1;1bb2
sequence:1ba2:.:.:.:.
MEDYTKIEKI GEGTYGVVYK GRHKTTGQVV AMKKIRLESE EEGVPSTAIR EISLLKELRH
PNIVSLQDVL MQDSRLYLIF EFLSMDLKKY LD-SIPPGQY*
Loop-005.py file
# Homology modelling by the automodel class
from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = './:../atom_files'
a = loopmodel(env,
alnfile = 'B04_2742_111_002.ali', # alignment filename
knowns = ('1ba4','1M8Qb'), # codes of the templates
sequence = '1ba2') # code of the target
a.starting_model= 1 # index of the first model
a.ending_model = 1 # index of the last model
# (determines how many models to calculate)
a.md_level = None # No refinement of model
a.loop.starting_model = 1 # First loop model
a.loop.ending_model = 1 # Last loop model
a.loop.md_level = refine.fast # Loop model refinement level
a.make() # do the actual homology modelling
Loop-005.log file
rdpir___648E> Alignment sequence not found in PDB file: 1 ../atom_files\1ba4.pdb
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