URL:
<http://gna.org/bugs/?22070>
Summary: Failure of the structure.superimpose user function
after deleting atoms with structure.delete.
Project: relax
Submitted by: bugman
Submitted on: Thu 22 May 2014 01:30:45 PM UTC
Category: relax's source code
Specific analysis category: None
Priority: 5 - Normal
Severity: 3 - Normal
Status: None
Assigned to: bugman
Originator Name:
Originator Email:
Open/Closed: Open
Release: 3.2.0
Discussion Lock: Any
Operating System: All systems
_______________________________________________________
Details:
The following user functions run from the base relax directory will trigger
the bug:
"""
path = 'test_suite/shared_data/frame_order/cam/'
pipe.create(pipe_name='superimpose', pipe_type='N-state', bundle=None)
structure.read_pdb(file='1J7P_1st_NH.pdb', dir=path, read_mol=None,
set_mol_name='C-dom', read_model=None, set_model_num=1, alt_loc=None,
verbosity=1, merge=False)
structure.read_pdb(file='1J7P_1st_NH_rot.pdb', dir=path, read_mol=None,
set_mol_name='C-dom', read_model=None, set_model_num=2, alt_loc=None,
verbosity=1, merge=False)
structure.delete(atom_id='@CA', verbosity=1, spin_info=True)
structure.superimpose(models=None, method='fit to first', atom_id=None,
centre_type='CoM', centroid=None)
"""
The error is:
relax> structure.superimpose(models=None, method='fit to first', atom_id=None,
centre_type='CoM', centroid=None)
Validating models:
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 569, 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 468, in
interact_script
exec_script(script_file, local)
File "/data/relax/relax-trunk/prompt/interpreter.py", line 347, 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/relax-trunk/fail.py", line 6, in <module>
structure.superimpose(models=None, method='fit to first', atom_id=None,
centre_type='CoM', centroid=None)
File "/data/relax/relax-trunk/prompt/uf_objects.py", line 223, in __call__
self._backend(*new_args, **uf_kargs)
File "/data/relax/relax-trunk/pipe_control/structure/main.py", line 910, in
superimpose
cdp.structure.validate_models()
File "/data/relax/relax-trunk/lib/structure/internal/object.py", line 2417,
in validate_models
atom_ref = "%-6s%5s %4s%1s%3s %1s%4s%1s %8s%8s%8s%6.2f%6.2f
%4s%2s%2s" % ('ATOM', mol_ref.atom_num[k],
self._translate(mol_ref.atom_name[k]), '',
self._translate(mol_ref.res_name[k]), self._translate(mol_ref.chain_id[k]),
self._translate(mol_ref.res_num[k]), '', '#', '#', '#', 1.0, 0,
self._translate(mol_ref.seg_id[k]), self._translate(mol_ref.element[k]), '')
IndexError: list index out of range
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?22070>
_______________________________________________
Message sent via/by Gna!
http://gna.org/
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-devel 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-devel
