Hi Michael,
As I said before, adding 'parser='scientific' solved this problem for me. I
had exactly the same error as the one you report. As Edward said, by
default, structure.read_pdb uses the internal reader so try to specify
explicitly the 'scientific' reader.
Cheers
Tiago Pais
-----Original Message-----
From: relax-users-bounces@xxxxxxx [mailto:relax-users-bounces@xxxxxxx] On
Behalf Of Michael Bieri
Sent: quarta-feira, 2 de Dezembro de 2009 21:34
To: relax-users@xxxxxxx
Subject: Error reading pdb file
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
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RE: Error reading pdb file