URL: <http://gna.org/bugs/?23288> Summary: Failure of the structure.read_pdb user function when simultaneously merging multiple molecules from one file. Project: relax Submitted by: bugman Submitted on: Tue 17 Feb 2015 08:43:02 AM UTC Category: relax's source code Specific analysis category: All analyses Priority: 3 - Low Severity: 2 - Minor Status: None Assigned to: bugman Originator Name: Originator Email: Open/Closed: Open Release: 3.3.6 Discussion Lock: Any Operating System: All systems _______________________________________________________ Details: The following two user function calls are sufficient to trigger this bug when running relax from the relax base directory: pipe.create(pipe_name='merge test', pipe_type='N-state') structure.read_pdb(file='2BE6_core_I_IV.pdb', dir='test_suite/shared_data/structures', read_mol=[1, 3], set_mol_name='CaM A', merge=True) This results in the error: Internal relax PDB parser. Opening the file 'test_suite/shared_data/structures/2BE6_core_I_IV.pdb' for reading. Traceback (most recent call last): File "<console>", line 1, in <module> File "/data/relax/relax-trunk/prompt/uf_objects.py", line 225, in __call__ self._backend(*new_args, **uf_kargs) File "/data/relax/relax-trunk/pipe_control/structure/main.py", line 1099, 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, alt_loc=alt_loc, verbosity=verbosity, merge=merge) File "/data/relax/relax-trunk/lib/structure/internal/object.py", line 2084, in load_pdb new_mol_name.append(set_mol_name[mol_index]) IndexError: list index out of range _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?23288> _______________________________________________ Message sent via/by Gna! http://gna.org/