Hi,
The answer to this question is simple. Say you have the runs called
'sphere', 'oblate spheroid', 'prolate spheroid', and 'ellipsoid'
(importantly with the diffusion tensor not fixed using fix('sphere',
'diff', fixed=0) as you would for optimising the diffusion tensors),
then for AIC model selection type:
model_selection('AIC', 'fin')
That's all that is necessary. The result of the model-selection will
be placed in the new run 'fin'. If you have additional runs in relax
then you will need to supply the 'runs' argument to the
model_selection() user function to exclude these. Hope this helps.
Cheers,
Edward
On 4/30/07, Hongyan Li <hylichem@xxxxxxxxxxxx> 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@xxxxxxxxx>:
> 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@xxxxxxxxxxxx> 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
Re: model selection