Error reading pdb file -- December 02, 2009 - 22:34

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

How can I solve this problem. It seems that it is pdb specific, as it 
worked for other structure files.

Cheers
Michael