'Re: model selection'

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List:       relax-users
Subject:    Re: model selection
From:       Clare-Louise Evans <pcxcle () domain ! hid>
Date:       2007-04-30 14:27:56
Message-ID: 4635FCEC.7050303 () domain ! hid
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Dear Douglas,

I kept getting this same error when I first tried using relax.  after 
checking all the input formats, it turned out to be that it wasn't 
finding the NH vectors because of the H atoms in my pdb.  I found simply 
changing the HN atoms to H rectified this.  Whether this was the true 
reason I'm unsure, but the error message stopped after I did this.

Hope this helps.

Clare

Douglas Kojetin wrote:
> While we are on the topic of model selection/optimization, I am  
> having some trouble with relax 1.2's full_analysis.py script.  I have  
> optimized the local_tm run, and I ran the initial run on the oblate  
> tensor (init).  When I attempt to optimize the oblate run (round_1),  
> I see the following error a:
>
> relax> results.write(run='final', file='results', dir='oblate/round_1/ 
> aic', force=1, format='columnar', compress_type=1)Opening the file  
> 'oblate/round_1/aic/results.bz2' for writing.RelaxError: The sequence  
> data for the run 'final' does not exist.
>
> Any ideas?
>
> Thanks,
> Doug
>
>
> On Apr 30, 2007, at 10:11 AM, Clare-Louise Evans wrote:
>
>   
>> Dear Edward,
>>
>> Sorry for the thread hijack, but I noticed in the PS section of the
>> quote Hongyan has included below your comment regarding convergence.
>>
>> I am having problems with convergence at the moment when running the
>> full_analysis.py script.  I have run the optimisation of the diffusion
>> models on the same PC.  For the oblate, prolate and ellipsoid models I
>> have failed to reach convergence after 30+ rounds.  The sphere model
>> converged within 5 rounds.  However, when I look at the output the  
>> only
>> difference between the chi-squared and other parameter values is in  
>> the
>> 10th and later decimal places.  Surely, with having such small
>> differences between the values they can be considered to have
>> converged.  However, in your comment you state they have to be
>> identical.  If this really is the case then I'm not sure how to  
>> proceed
>> given that I'm failing to reach convergence on these 3 models?
>>
>> Apologies if this ties in to the question I asked yesterday regarding
>> full_analysis.py.
>>
>> Kind regards
>> Clare
>>
>> Hongyan Li wrote:
>>     
>>> Dear Edward,
>>> Thanks for your early suggestion regarding different model  
>>> selections. I have
>>> been busy on other stuff and only recently got time to focus on  
>>> this subject
>>> again.
>>> I have run all the diffusion models e.g. isotropic, prolate,  
>>> oblate and
>>> ellipsoid and model selections were made within each model (in aic  
>>> directory).
>>> I am not sure how to write a script to select different models using
>>> 'model_selection()'. Could you please do me a favor?
>>> Your help is highly appreciated!
>>> Best wishes,
>>> Hongyan
>>>
>>> Quoting Edward d'Auvergne <edward.dauvergne@domain.hid>:
>>>
>>>
>>>       
>>>> Hi,
>>>>
>>>> To compare the results what you need to employ is a technique  
>>>> from the
>>>> statistical field of model selection.  The spherical diffusion
>>>> (isotropic) + all model-free models of all selected residues is one
>>>> single mathematical model.  The prolate and oblate spheroids  
>>>> (prolate
>>>> and oblate axially symmetric anisotropic diffusion tensors) + all
>>>> model-free models, and the ellipsoid (fully anisotropic or three
>>>> different eigenvalues) + all model-free models, are three additional
>>>> mathematical models.  Therefore to compare these four different  
>>>> models
>>>> you need to select the model which best represents your relaxation
>>>> data.  These models are, however, not nested and therefore cannot be
>>>> compared using ANOVA F-tests!  Firstly the three types of diffusion
>>>> tensor are not nested (there is a reference from Dominique Marion's
>>>> group in which they say ANOVA statistics cannot be used but I can't
>>>> find it at the moment (although it shouldn't be too hard to track
>>>> down, it's related to Tensor)).  Secondly the model-free models
>>>> selected will be different between the four models.  Hence chi- 
>>>> squared
>>>> and F-tests cannot be used.
>>>>
>>>> A useful reference (I'm not at all biased ;) for this problem is my
>>>> paper d'Auvergne, E. J. and Gooley, P. R. (2003), (see
>>>> http://www.nmr-relax.com/refs.html for the full reference).  On page
>>>> 37 at the end of that paper I discuss how AIC model selection is
>>>> perfect for selecting between these non-nested models.  The AIC
>>>> criterion is still
>>>>
>>>> AIC = chi2 + 2k,
>>>>
>>>> however chi2 is the minimised chi-squared value for the complete  
>>>> model
>>>> and k is the sum of the number of diffusion parameters and number of
>>>> model-free parameters for all spin systems.  BIC model selection is
>>>> likely to work quite well as well.  If you have four runs, one for
>>>> each of the diffusion models, then the relax user function
>>>> 'model_selection()' is designed to select between these models.  I
>>>> hope this helps and hasn't been too biased.
>>>>
>>>> Cheers,
>>>>
>>>> Edward
>>>>
>>>>
>>>> P.S.  Prior to model selection between the diffusion models, the
>>>> diffusion models must have fully converged.  Multiple iterations of
>>>> optimisation of the model-free models, AIC model selection, and
>>>> optimisation of all parameters together (diffusion tensor + model- 
>>>> free
>>>> parameter of all residues) must be executed.  Convergence is when  
>>>> two
>>>> iterations possess identical chi-squared values, identical model- 
>>>> free
>>>> models, and identical parameter values.
>>>>
>>>>
>>>> On 3/2/07, Hongyan Li <hylichem@domain.hid> wrote:
>>>>
>>>>         
>>>>> Dear relax users,
>>>>> I have managed to use Relax to run my dynamics data by both  
>>>>> isotropic and
>>>>> axial-oblate models. My qestion is how to compare the results, by
>>>>>
>>>>>           
>>>> chi-square??
>>>>
>>>>         
>>>>> what is the criteria to make judgment that which residues is beter
>>>>>
>>>>>           
>>>> simulated
>>>>
>>>>         
>>>>> with which model?
>>>>>
>>>>> Thanks for your kind help!
>>>>>
>>>>> Best wishes,
>>>>>
>>>>> Hongyan
>>>>>
>>>>> Dr. Hongyan Li
>>>>> Department of Chemistry
>>>>> The University of Hong Kong
>>>>> Pokfulam Road
>>>>> Hong Kong
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> relax (http://nmr-relax.com)
>>>>>
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>>>>>
>>>>>
>>>>>           
>>> Dr. Hongyan Li
>>> Department of Chemistry
>>> The University of Hong Kong
>>> Pokfulam Road
>>> Hong Kong
>>>
>>>
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