Re: [bug #13259] full analysis-high Te values -- March 26, 2009 - 16:37

Hi,

The bug you see there is the regression.  I'm working on the fix right
now.  Should have some code to test soon.

Cheers,

Edward


On Thu, Mar 26, 2009 at 4:26 PM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:
> Hi Ed,
>
> Pierre-Yves and I are now testing the fix...
>
> We set-up three different tests including all datasets (for all ~150
> residues). After the first round of prolate completed, we will know if
> residue 44 is still associated with a ts of ~20 ns in model 'm8' or if this
> model is eliminated...
>
> 1.
> Start from scratch with full_analysis.py. The local_tm run will be done and,
> after, the prolate run.
>
> 2.
> Use the old local_tm directory (from analysis before the bug report of
> yesterday) and only make the prolate run...
>
> 3.
> Use the old prolate directory (from analysis before the bug report of
> yesterday) including the init and round_1 sub-directories and only make
> round 2.
>
> We will have to wait to see if everything looks normal.
>
> However, there seems to be a problem, already. For test #2, we get the
> following error in the inital round of optimisation for the diffusion tensor
> (init round):
>
> ==============
> relax> diffusion_tensor.init(params=(1e-08, 0, 0, 0), time_scale=1.0,
> d_scale=1.0, angle_units='deg', param_types=0, spheroid_type='prolate',
> fixed=False)
>
> relax> fix(element='all_spins', fixed=True)
>
> relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
> verbosity=1)
> The diffusion tensor parameters together with the model-free parameters for
> all spins will be used.
> Unconstrained grid search size:
> 3483241635926760276239670296061783033856385373964443346380512727207030807448244020315627244532223540371618455651157976598330893796730564039193972812374440994792715667315064916696072753116546554132476003724628552320667084135787252303417928004684992625923335554734448200360162656232011377981776056433588143239686879331L
> (constraints may decrease this size).
>
> RelaxError: A grid search of size
> 3483241635926760276239670296061783033856385373964443346380512727207030807448244020315627244532223540371618455651157976598330893796730564039193972812374440994792715667315064916696072753116546554132476003724628552320667084135787252303417928004684992625923335554734448200360162656232011377981776056433588143239686879331L
> is too large.
> ==============
>
> This problem also arises when not making the change at line 303
> (self.model_selection(modsel_pipe='final', dir=self.base_dir + 'aic')).
>
> So, my guess is that this problem might be due to changes in r8999.
>
> Regards,
>
>
> Séb  :)
>
>
>
>
> Edward d'Auvergne wrote:
> > Actually, this will cause a problem.  I've closely looked at the
> > script, and it appears that your suggestion is correct:
> >
> >
> > > > > > > I just tried something using the files in the bug report, as well as
> > > > > > > with
> > > > > > > the up-to-date 1.3 repository (r9001)...
> > > > > > >
> > > > > > > I modified line 303 of the script from:
> > > > > > >
> > > > > > >                   self.model_selection(modsel_pipe='final',
> > > > > > > dir=self.base_dir + 'aic')
> > > > > > >
> > > > > > > to:
> > > > > > >
> > > > > > >                   self.model_selection(modsel_pipe='aic',
> > > > > > > dir=self.base_dir + 'aic')
> > > > > > >
> > > > > > > With this change, model 'm8' is eliminated and model 'm1' is selected
> > > > > > > instead.
> >
> > This data pipe is for AIC model selection and the results go into the
> > 'aic' directory.  This is followed by the 'opt' data pipe for
> > diffusion tensor optimisation.  So I'll make the change to the
> > repository.  But could you check if all works with the changes that
> > were made to the 1.3 line?  I think these changes were logical, but
> > there is a regression causing a system test to fail.
> >
> > Cheers,
> >
> > Edward
>
>
> --
> Sébastien Morin
> PhD Student
> S. Gagné NMR Laboratory
> Université Laval & PROTEO
> Québec, Canada