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"
On 11/16/2010 07:34 AM, Felipe Villanelo wrote: > I'm trying of add some residues to an multimeric PDB, with a very simple > model script: ... > But after a short run, the program crash with tue following message: ... > _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)
I would need to see your input files to be 100% sure, but my best guess is that if you look at line 2404 of that modelo4-Al.ini file, rather than atom coordinates you will see asterisks (****). Because PDB is a fixed-width format, any coordinates larger than 9999 (or smaller than -999) cannot be represented, and probably what is happening is that your very long insertion (which Modeller will initially generate as a simple extended chain, since it has no additional information) ends up with such large coordinates.
I suggest that you don't try to model that 40 aa region at all - Modeller will not be able to generate a good model anyway.
I will fix this "properly" in a future release, but if you really want to try to model that insertion, you can take that bad .ini file, put in proper coordinates using a text editor (even replacing each *** with zero coordinates would be an improvement, but sensible coordinates would be best) and then rerun your script, using the 'inifile' keyword to force use of your "fixed" initial model: http://salilab.org/modeller/9v8/manual/node26.html
If your problem is something different (no asterisks in your PDB file) then please send me your input files so I can reproduce your problem.
Ben Webb, Modeller Caretaker
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Felipe Villanelo -
Modeller Caretaker