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
