Hi, Would you be able to file a bug report? Cheers. It would be very useful to come up with a truncated PDB file that gives exactly the same error. 3 or 4 lines would be perfect. This really helps in isolating the bug. I'm not sure what this error could be because I have never seen anything like it before.
Cheers, Edward 2009/12/2 Michael Bieri <[email protected]>: > 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. > > This error only occurs by executing models sphere - ellipsoid. there was > no error when launching local_tm. > > How can I solve this problem. It seems that it is pdb specific, as it > worked for other structure files. > > Cheers > Michael > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users mailing list > [email protected] > > 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-users > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] 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-users
