Update of bug #21814 (project relax):
Status: None => Confirmed
_______________________________________________________
Follow-up Comment #1:
The following error occurs when loading the SpUreE_dimer_H_new.pdb and
hadded_2.pdb PDB files (but not the SpUreE_dimer_H.pdb file):
relax> pipe.create(pipe_name='bug_21814', pipe_type='mf', bundle=None)
relax> structure.read_pdb(file='hadded_2.pdb', dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, alt_loc=None,
merge=False)
Internal relax PDB parser.
Opening the file 'hadded_2.pdb' for reading.
Traceback (most recent call last):
File "/data/relax/relax-trunk/multi/processor.py", line 494, in run
self.callback.init_master(self)
File "/data/relax/relax-trunk/multi/__init__.py", line 318, in
default_init_master
self.master.run()
File "/data/relax/relax-trunk/relax.py", line 194, in run
self.interpreter.run(self.script_file)
File "/data/relax/relax-trunk/prompt/interpreter.py", line 275, in run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/data/relax/relax-trunk/prompt/interpreter.py", line 578, in
run_script
return console.interact(intro, local, script_file,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/data/relax/relax-trunk/prompt/interpreter.py", line 477, in
interact_script
exec_script(script_file, local)
File "/data/relax/relax-trunk/prompt/interpreter.py", line 352, in
exec_script
runpy.run_module(module, globals)
File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
fname, loader, pkg_name)
File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/data/relax/debugging/bug_21814/test.py", line 4, in <module>
structure.read_pdb('hadded_2.pdb')
File "/data/relax/relax-trunk/prompt/uf_objects.py", line 221, in __call__
self._backend(*new_args, **uf_kargs)
File "/data/relax/relax-trunk/pipe_control/structure/main.py", line 722, 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 1813,
in load_pdb
pdb_lines = self._parse_pdb_ss(pdb_lines)
File "/data/relax/relax-trunk/lib/structure/internal/object.py", line 500,
in _parse_pdb_ss
record_type, strand, sheet_id, num_strands, init_res_name, init_chain_id,
init_seq_num, init_icode, end_res_name, end_chain_id, end_seq_num, end_icode,
sense, cur_atom, cur_res_name, cur_chain_id, cur_res_seq, cur_icode,
prev_atom, prev_res_name, prev_chain_id, prev_res_seq, prev_icode =
pdb_read.sheet(lines[i])
File "/data/relax/relax-trunk/lib/structure/pdb_read.py", line 1221, in
sheet
fields.append(record[49])
IndexError: string index out of range
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?21814>
_______________________________________________
Message sent via/by Gna!
http://gna.org/
[bug #21814] PDB file format