This all sounds good. I also like the idea that users can add more iterations. I will recode this. Why do you want to get rid of the BIC selection mode? Even recent papers are still using it and as relax can handle it, I would suggest not to force users too much to use AIC. What do you think?
Edward d'Auvergne wrote: > The local tm model for a peptide is highly probable because of high > internal mobility being coupled to the external diffusion. I would > guess that in this case the protocol was circling endlessly around the > solution. We should store all the information (already converted for > comparison to save a little computation time) for each iteration > within lists from the convergence() method. For a maximum number, I > would suggest 30. Each iteration is much quicker to complete than the > previous, so 20 vs. 30 is much quicker than the first or second 10. > It would be better to be on the safe side and have a max of 30 - it is > too difficult for us to predict how a difficult, yet solvable case > will look like. In this case, I think we should add an new list > called self.max_iterations which starts as false for all. If 30 > iterations is hit, then the position for that model should be set to > True. I would also recommend removing the unused AIC vs. BIC GUI > element and maybe replacing it with a text box where the user can > change this number (and we only allow it to be bigger than 30 ;). > > The self.max_iterations list is then used in the model_selection() > method to eliminate that global model prior to model selection. For > the progress bar, it would be good to have the iteration number also > displayed. That way it is better communicated that the bar is > counting iterations and not a percentage of being complete. We > shouldn't give to the user the impression that they have to wait until > the progress bar hits the end. What kindm of granularity do you have > here? Can we have a movement for the completion of each iteration? > > Regards, > > Edward > > > > > On 13 April 2010 00:20, Michael Bieri <[email protected]> wrote: > >> It would be the best to store results of each iterations in >> convergence(). I already had a couple of cases / models that never >> converged. Predominately, these were molecules with a high degree o >> motion. For example there was a peptide (40 residues), where none of the >> models converged after 20 iterations, so I aborted them. The diffusion >> tensor fits well so I thought that's alright. I heard from other people >> that they also stop their calculation after 20 iterations. Nevertheless >> and surprisingly, the model wich was selected for S2 (And the rest) was >> local tm - possible? >> >> But in general I like the idea to compare the minimization of all the >> iterations, as you suggested. I still would set a maximum of 20 (or 30) >> iterations to avoid calculations over several days. Another benefit is >> that we are able to update the progress bar. >> >> >> Edward d'Auvergne wrote: >> >>> Hi Michael, >>> >>> We could add an arg to limit the number of iterations, but I think >>> there is a much better way. The problem of iterating forever is >>> because of circling around the minimum (not the optimisation minimum >>> but Occam's razor, as described in equation (14) of my 2007 paper >>> http://www.nmr-relax.com/refs.html). Currently only the current to >>> previous iterations are compared, but some people have encountered a 3 >>> iteration cycle. Even larger looping might occur. Note that the >>> repeated position in this cycle is identical to one of the previous. >>> So we should really store all of the required info in the >>> convergence() method of auto_analyses/dauvergne_protocol.py and check >>> the current against all iterations. >>> >>> If one of these converged loops has not been reached after 20 >>> iterations, then either the system is complex but will still soon >>> converge, or something is seriously, very seriously wrong. The model >>> should be deselected and the user told of its total failure. My >>> experience is that after 20, convergence has been reached. But I >>> think we should allow more before termination, as the termination is a >>> sign that something is sick. >>> >>> If we catch the large iteration circling about Occam's razor and >>> terminate, do you think we would need a maximum iteration termination >>> point and subsequent global model elimination? Have you encountered >>> such a non-cycling, infinite looping? >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> On 12 April 2010 03:02, <[email protected]> wrote: >>> >>> >>>> Author: michaelbieri >>>> Date: Mon Apr 12 03:02:19 2010 >>>> New Revision: 11061 >>>> >>>> URL: http://svn.gna.org/viewcvs/relax?rev=11061&view=rev >>>> Log: >>>> The relaxGUI controller updates its progress bar using informations from >>>> the status singleton during model-free analysis. >>>> >>>> Currently, there is a maximum of iterations set for models 1 - 5. This >>>> also has to be set in the dauvergne_protocol.py script. Edward, what do >>>> you think about limiting to 20 iterations? >>>> >>>> Modified: >>>> branches/bieri_gui/gui_bieri/controller.py >>>> >>>> Modified: branches/bieri_gui/gui_bieri/controller.py >>>> URL: >>>> http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/controller.py?rev=11061&r1=11060&r2=11061&view=diff >>>> ============================================================================== >>>> --- branches/bieri_gui/gui_bieri/controller.py (original) >>>> +++ branches/bieri_gui/gui_bieri/controller.py Mon Apr 12 03:02:19 2010 >>>> @@ -142,13 +142,50 @@ >>>> >>>> def __init__(self,aWxTextCtrl): >>>> self.out=aWxTextCtrl >>>> + self.status = Status() >>>> >>>> + def limit_entries(self): >>>> + """ Function to overcome feedback problem of wx.CallAfter() >>>> command""" >>>> + >>>> + # Maximum allowed number of lines in log window. >>>> + max_entries = 10000 >>>> + >>>> + # read number of lines in log window. >>>> + total_entries = self.out.log_panel.GetNumberOfLines() >>>> + >>>> + # Shift entries backwards if maximum of line exeeded. >>>> + if total_entries > max_entries: >>>> + # Reset log window entries >>>> + new_entries = 'Refreshing log window...\n\n' >>>> + self.out.log_panel.SetValue(new_entries) >>>> >>>> def write(self,string): >>>> - global progress >>>> >>>> # Limit panle entries to max_entries Lines. >>>> wx.CallAfter(self.limit_entries) >>>> + >>>> + # Update Gauge (Progress bar). >>>> + # Local tm model: >>>> + if self.status.dAuvergne_protocol.diff_model == 'local_tm': >>>> + # Current model. >>>> + no = self.status.dAuvergne_protocol.current_model[2:] >>>> + no = int(no) >>>> + >>>> + # Total selected models. >>>> + total_models = >>>> len(self.status.dAuvergne_protocol.local_mf_models) >>>> + >>>> + # update Progress bar. >>>> + wx.CallAfter(self.out.progress_bar.SetValue, >>>> (100*no/total_models)) >>>> + >>>> + # Sphere to Ellipsoid Models. >>>> + if self.status.dAuvergne_protocol.diff_model in ['sphere', >>>> 'prolate', 'oblate', 'ellipsoid']: >>>> + # Determine actual round (maximum is 20). >>>> + wx.CallAfter(self.out.progress_bar.SetValue, >>>> (100*(self.status.dAuvergne_protocol.round-1)/20)) >>>> + >>>> + # Final analysis. >>>> + if self.status.dAuvergne_protocol.diff_model == 'final': >>>> + mc_simulation = self.status.mc_number >>>> + >>>> >>>> # Add new output. >>>> wx.CallAfter(self.out.log_panel.AppendText, string) >>>> >>>> >>>> _______________________________________________ >>>> relax (http://nmr-relax.com) >>>> >>>> This is the relax-commits 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-commits >>>> >>>> >>>> >>> _______________________________________________ >>> relax (http://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 >>> >>> >>> >>> >> _______________________________________________ >> relax (http://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 >> >> > > > _______________________________________________ relax (http://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
