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>
_______________________________________________
Nachricht geschickt von/durch Gna!
http://gna.org/
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-devel mailing list
relax-devel@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-devel