Re: Nested exception from sub processor -- October 11, 2011 - 21:53

Thank you, Edward (no problem about the delay). I have submitted the
bug report (#18807). I am just curious: is there any practical use for
the "ave=False" flag then?
As far as my data analysis goes, I can separate the NMR ensemble into
the individual models and run the calculations on each of them. Does
this sound like a reasonable approach?

Vitaly

On Tue, Oct 11, 2011 at 14:39, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Hi,
>
> Sorry for the delay there.  I've been quite busy lately.  The problem
> is that I'm pretty sure that the model-free analysis is not set up to
> handle multiple vectors.  This lies within the theory itself.  The
> bond vector should be in the centre of the cone or whatever the vector
> distribution is.  To be able to use multiple vectors would require
> digging into the model-free theory and modifying it.  Therefore the
> vectors should be averaged or a single structure used.  I am surprised
> that relax allows the calculation to start without a RelaxError being
> thrown.  I will modify the code later to give such an error and
> prevent the calculation from starting.  Thanks for pointing out this
> error.  If you could submit it as a bug to
> https://gna.org/bugs/?func=additem&group=relax, that would be very
> useful if some else encounters the same problem.
>
> Cheers,
>
> Edward
>
>
> On 11 October 2011 21:29, V.V. <vvostri@xxxxxxxxx> wrote:
> > 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.