Re: [bug #14876] Error reading pdb file -- December 04, 2009 - 00:28

Hi Edward

Thank you for your advice. The pdb file was read after deleting the TER 
lines.
But there are no NH atoms.... How could you analyze this data? Do you 
have another 1F35.pdb file that contains hydrogens? The one from pdb.org 
does not have any hydrogens (maybe 10...).

Cheers
Michael

Edward d'Auvergne schrieb:
> Hi,
>
> I've had a look at the file and as far as I can tell, it has corrupted
> the PDB format.  There are TER records in the middle of the protein?!?
>  These are before MSE residues!  According to
> http://www.wwpdb.org/documentation/format32/sect9.html#TER (PDB format
> - Atomic Coordinate Entry Format Version 3.2), "The TER record
> indicates the end of a list of ATOM/HETATM records for a chain."  But
> in this file TER is not the end of the chain.  This is a clear and
> blatant violation of the PDB standard!  Retards!  So I really don't
> know how to handle this, or how common this is.  I'm trying to repair
> this file by deleting the TER records, to see what that will do.
>
> Regards,
>
> Edward
>
>
> 2009/12/2 Michael Bieri <NO-REPLY.INVALID-ADDRESS@xxxxxxx>:
>   
> > URL:
> >  <http://gna.org/bugs/?14876>
> >
> >                 Summary:  Error reading pdb file
> >                 Project: relax
> >            Submitted by: michaelbieri
> >            Submitted on: Mittwoch 02.12.2009 um 22:13
> >                Category: relax's source code
> >                Severity: 3 - Normal
> >                Priority: 5 - Normal
> >                  Status: None
> >                 Privacy: Public
> >             Assigned to: None
> >         Originator Name:
> >        Originator Email:
> >             Open/Closed: Open
> >         Discussion Lock: Any
> >                 Release: 1.3.4
> >        Operating System: GNU/Linux
> >
> >    _______________________________________________________
> >
> > Details:
> >
> > By executing the full_analysis.py script, I get an error message after
> > reading the pdb file (structure.read_pdb(PDB_FILE)). This does not occur
> > using the local_tm model.
> >
> > This error occurs using relax 1.3.4 as well as the current 1.3 line. No error
> > occurs by running relax 1.3.3.
> >
> >
> > 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
> >
> >
> >
> > Cheers
> > Michael
> >
> >
> >
> >    _______________________________________________________
> >
> > File Attachments:
> >
> >
> > -------------------------------------------------------
> > Date: Mittwoch 02.12.2009 um 22:13  Name: 1F35_mono.pdb  Size: 106kB   By:
> > michaelbieri
> > pdb file. Monomer extracted using pymol
> > <http://gna.org/bugs/download.php?file_id=7430>
> >
> >    _______________________________________________________
> >
> > Reply to this item at:
> >
> >  <http://gna.org/bugs/?14876>
> >
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> >  http://gna.org/
> >
> >
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