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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