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/