Re: Error reading pdb file -- December 02, 2009 - 22:55

Hi,

Would you be able to file a bug report?  Cheers.  It would be very
useful to come up with a truncated PDB file that gives exactly the
same error.  3 or 4 lines would be perfect.  This really helps in
isolating the bug.  I'm not sure what this error could be because I
have never seen anything like it before.

Cheers,

Edward



2009/12/2 Michael Bieri <michael.bieri@xxxxxx>:
> Hi
> I have an error message by running the full analysis script after the
> command:
>
> structure.read_pdb(PDB_FILE)
>
>
> The error message is:
>
> Internal relax PDB parser.
> Opening the file '/home/michael/Desktop/LinuxBox/OMP/1F35_mono.pdb' for
> reading.
> RelaxWarning: The atom number 80 from the CONECT record cannot be found
> within the ATOM and HETATM records.
> RelaxWarning: The atom number 88 from the CONECT record cannot be found
> within the ATOM and HETATM records.
> Traceback (most recent call last):
>  File "relaxGUI.py", line 4126, in exec_model_free
>   start_model_free(self, which_model)
>  File "relaxGUI.py", line 1533, in start_model_free
>   Model()
>  File "relaxGUI.py", line 1125, in __init__
>   structure.read_pdb(PDB_FILE)
>  File "/home/michael/Programme/relax-1.3/prompt/structure.py", line 464,
> in read_pdb
>   generic_fns.structure.main.read_pdb(file=file, dir=dir,
> read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model,
> set_model_num=set_model_num, parser=parser)
>  File "/home/michael/Programme/relax-1.3/generic_fns/structure/main.py",
> line 355, in read_pdb
>   cdp.structure.load_pdb(file_path, read_mol=read_mol,
> set_mol_name=set_mol_name, read_model=read_model,
> set_model_num=set_model_num, verbosity=verbosity)
>  File
> "/home/michael/Programme/relax-1.3/generic_fns/structure/internal.py",
> line 674, in load_pdb
>   mol.fill_object_from_pdb(mol_records)
>  File
> "/home/michael/Programme/relax-1.3/generic_fns/structure/internal.py",
> line 1419, in fill_object_from_pdb
>   self.atom_connect(index1=self.__atom_index(record[1]),
> index2=self.__atom_index(record[i+2]))
>  File
> "/home/michael/Programme/relax-1.3/generic_fns/structure/internal.py",
> line 1378, in atom_connect
>   if index2 not in self.bonded[index1]:
> TypeError: list indices must be integers, not NoneType
>
>
>
> This error occurs with the relax 1.3.4 release as wells as with the
> latest 1.3 repository line (svn co svn://svn.gna.org/svn/relax/1.3).
> The pdb file is read correctly by using relax 1.3.3.
>
> This error only occurs by executing models sphere - ellipsoid. there was
> no error when launching local_tm.
>
> How can I solve this problem. It seems that it is pdb specific, as it
> worked for other structure files.
>
> Cheers
> Michael
>
>
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