Re: Nested exception from sub processor -- October 11, 2011 - 21:30

Looks like it is an issue with "ave=False" flag in
"structure.vectors", rather then "deselect.read". The NMR ensemble I
have consists of two structured domains, connected with a flexible
loop, i.e. the overall RMSD is fairly high and the N-H vectors in
different models are likely to be quite different. Can this be the
reason for the previously mentioned exception?

Thank you,
Vitaly


On Fri, Oct 7, 2011 at 15:28, V.V. <vvostri@xxxxxxxxx> wrote:
> Hi Edward,
>
> I am running "dauvergne_protocol" script for my protein. The
> "local_tm" and "sphere" models calculations proceeded fine, but with
> prolate/oblate/ellipsoid diffusion tensors an exception is thrown (the
> output is below). I have run the same script successfully before. The
> difference is that I have excluded several mobile residues and using
> "ave=False" in "structure.vectors" (the pdb file is an NMR ensemble,
> 20 models). If necessary, I can send the input files separately. Relax
> revision is 14809.
>
> Thank you,
> Vitaly
>
> Traceback (most recent call last):
>  File "/home/vitalyv/relax/multi/uni_processor.py", line 136, in run
>    self.callback.init_master(self)
>  File "/home/vitalyv/relax/multi/processor.py", line 263, in
> default_init_master
>    self.master.run()
>  File "/home/vitalyv/relax/relax.py", line 174, in run
>    self.interpreter.run(self.script_file)
>  File "/home/vitalyv/relax/prompt/interpreter.py", line 300, in run
>    return run_script(intro=self.__intro_string, local=locals(),
> script_file=script_file, quit=self.__quit_flag,
> show_script=self.__show_script,
> raise_relax_error=self.__raise_relax_error)
>  File "/home/vitalyv/relax/prompt/interpreter.py", line 610, in run_script
>    return console.interact(intro, local, script_file, quit,
> show_script=show_script, raise_relax_error=raise_relax_error)
>  File "/home/vitalyv/relax/prompt/interpreter.py", line 495, in 
> interact_script
>    exec_script(script_file, local)
>  File "/home/vitalyv/relax/prompt/interpreter.py", line 383, in exec_script
>    runpy.run_module(module, globals)
>  File "/usr/lib/python2.7/runpy.py", line 180, in run_module
>    fname, loader, pkg_name)
>  File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
>    exec code in run_globals
>  File "/home/vitalyv/relax/wtpln/dauvergne_protocol.py", line 218, in 
> <module>
>    dAuvergne_protocol(pipe_name=name, diff_model=DIFF_MODEL,
> mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS,
> grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM,
> conv_loop=CONV_LOOP)
>  File "/home/vitalyv/relax/auto_analyses/dauvergne_protocol.py", line
> 223, in __init__
>    self.execute()
>  File "/home/vitalyv/relax/auto_analyses/dauvergne_protocol.py", line
> 596, in execute
>    self.interpreter.grid_search(inc=inc)
>  File "/home/vitalyv/relax/prompt/minimisation.py", line 106, in grid_search
>    minimise.grid_search(lower=lower, upper=upper, inc=inc,
> constraints=constraints, verbosity=verbosity)
>  File "/home/vitalyv/relax/generic_fns/minimise.py", line 146, in 
> grid_search
>    processor_box.processor.run_queue()
>  File "/home/vitalyv/relax/multi/uni_processor.py", line 149, in run_queue
>    command.run(self, completed)
>  File 
> "/home/vitalyv/relax/specific_fns/model_free/multi_processor_commands.py",
> line 144, in run
>    raise Capturing_exception(rank=processor.rank(), 
> name=processor.get_name())
> Capturing_exception:
>
> ------------------------------------------------------------------------------------------------------------------------
>
>  File 
> "/home/vitalyv/relax/specific_fns/model_free/multi_processor_commands.py",
> line 132, in run
>    results = self.optimise()
>  File 
> "/home/vitalyv/relax/specific_fns/model_free/multi_processor_commands.py",
> line 185, in optimise
>    results = grid_point_array(func=self.mf.func, args=(),
> points=self.opt_params.subdivision,
> verbosity=self.opt_params.verbosity)
>  File "/usr/lib/python2.7/site-packages/minfx/grid.py", line 282, in
> grid_point_array
>    f = func(*(points[k],)+args)
>  File "/home/vitalyv/relax/maths_fns/mf.py", line 517, in func_diff
>    self.diff_data.calc_ci(data, self.diff_data)
>  File "/home/vitalyv/relax/maths_fns/weights.py", line 80, in 
> calc_spheroid_ci
>    data.ci[0] = 0.25 * data.three_dz2_one**2
>
>
> Nested Exception from sub processor
> Exception type: ValueError
> Message: setting an array element with a sequence.