[modeller_usage] Error in ini modeller-generated file

[Felipe Villanelo <>]

Hi all, 

I'm trying of add some residues to an multimeric PDB, with a very simple model script:

env = environ()
env.io.hetatm = True
env.io.atom_files_directory = ['.', '../../atom_files']

a = automodel(env, alnfile='modelo4-2.ali',
              knowns=('fil1','fil2'), sequence='modelo4-Al')
a.starting_model = 1
a.ending_model = 1
a.make()

But after a short run, the program crash with tue following message:

Traceback (most recent call last):
  File "model2.py", line 32, in ?
    a.make()
  File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line 109, in make
    self.multiple_models(atmsel)
  File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line 215, in multiple_models
    self.outputs.append(self.single_model(atmsel, num))
  File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line 280, in single_model
    self.randomize_initial_structure(atmsel)
  File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line 246, in randomize_initial_structure
    self.read_initial_model()
  File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line 242, in read_initial_model
    self.read(file=self.inifile, io=io)
  File "/usr/lib/modeller9v8/modlib/modeller/model.py", line 117, in read
    model_format, model_segment)
_modeller.FileFormatError: read_pd_702E> File: modelo4-Al.ini, Line    2404 Could not parse data from file; file is probably corrupt.


Curiosily, the 'modelo4-Al.ini' file is generated by modeller during the run, and I cannot bypass this problem
The alignment file is ok. 
Maybe the problem is, that there is a ~40 Aa coil with no-template sequence to model (between other ssequences with template)

Any suggestion will help
Thanks


Felipe Villanelo Lizana
Bioquímico
Laboratorio de Biología Estructural y Molecular
Universidad de Chile

"La curiosidad no mató al gato, sino que la falta de ella"