Hi, This model selection technique is called Akaike's Information Criteria (AIC). See http://www.nmr-relax.com/refs.html#dAuvergneGooley03 for details on this. How would you produce a plot in Grace of the models selected? I don't know how this would work for the dispersion models. In a model-free analysis I have deliberately taken the decision to not create such a plot. In model-free, relax supports models m0 to m9, so these could be plotted as 0 to 9 on the Y-axis. But this is not done and will never be implemented. The reason is because the information about which model is selected is worthless. What is important is the dynamics extracted. This is especially the case of nested models. Just because a parameter is missing from a model, this does not mean that it is not present. For example there are model-free models without the Rex parameter. If these are selected, this does not mean that Rex is not present. It means that Rex is statistically insignificant in the current data set. Model differences are an academic question and is not interesting in practice. Sometimes the AIC value for two nested models is very similar and that means that the parameter different between the two is sitting directly on the boarder of statistical significance/insignificant. You could pick either model and it should not make a statistical difference in the dynamics picture. It does not relate to the dynamics, just the judgement of statistically significance for parameters. Therefore for practical reasons, for model-free at least, the interesting plots, text files, and PyMOL/MOLMOL macros are of the parameter values themselves. I think is would be much more of interest to implement PyMOL/MOLMOL macros for the dispersion parameters so you can see the dynamics directly on the 3D structure. This is performed in NESSY and needs to be added to relax.
Also note that when you are analysing data, you would probably limit the number of models to 2-3. For example if you know that all residues are experiencing slow exchange, the LM63 fast exchange model does not need to be used. It is interesting to see that sometimes the analytic models are selected and sometimes the numeric models. But this is an academic curiosity, it is probably not a practical question anyone analysing real dispersion data is interested in. The way an analysis would normally be performed is to first decide if the analytic or numeric approach is to be used. For the analytic approach with slow exchange, you only need the 'No Rex' and 'CR72' models. You could add the 'IT99' model if you can see that pA >> pB in the spectra, i.e. the pB peak is tiny. If you take the numeric approach, then the 'No Rex' and 'NS 2-site expanded' models can be used. Once you perform an initial analysis of all residues separately, you can then look at the dynamics parameter values and judge which spins to cluster together to have the same model of dynamics, then re-perform the analysis. Regards, Edward On 28 August 2013 12:02, Troels Emtekær Linnet <[email protected]> wrote: > Hi. > > After a AIK selection between models > > CR72/ > IT99/ > LM63/ > NS 2-site expanded/ > > I get this selected list of models. > Would it be possible to add to the grace images in the final directory, > the selected model and the residue number? > > 3 LM63 > 4 CR72 > 5 NS 2-site expanded > 6 CR72 > 7 LM63 > 8 No Rex > 9 NS 2-site expanded > 10 CR72 > 11 LM63 > 12 CR72 > 13 IT99 > 14 NS 2-site expanded > 15 NS 2-site expanded > 16 LM63 > 17 CR72 > 18 CR72 > 20 NS 2-site expanded > 21 NS 2-site expanded > 22 CR72 > 23 LM63 > 24 LM63 > 25 CR72 > 26 IT99 > 27 NS 2-site expanded > 28 NS 2-site expanded > 29 CR72 > 30 NS 2-site expanded > 31 CR72 > 32 CR72 > 33 IT99 > 34 IT99 > 35 IT99 > 36 IT99 > 37 IT99 > 38 NS 2-site expanded > 39 LM63 > 40 No Rex > 41 CR72 > 42 No Rex > 43 NS 2-site expanded > 45 IT99 > 46 CR72 > 47 CR72 > 48 IT99 > 49 NS 2-site expanded > 50 LM63 > 51 NS 2-site expanded > 52 CR72 > 53 NS 2-site expanded > 54 NS 2-site expanded > 55 No Rex > 56 IT99 > 57 LM63 > 58 LM63 > 59 NS 2-site expanded > 60 CR72 > 61 IT99 > 62 NS 2-site expanded > 63 NS 2-site expanded > 64 CR72 > 65 IT99 > 66 No Rex > 67 CR72 > 68 No Rex > 69 NS 2-site expanded > 70 NS 2-site expanded > 71 NS 2-site expanded > 72 NS 2-site expanded > 73 LM63 > 74 LM63 > 75 NS 2-site expanded > 76 NS 2-site expanded > 77 IT99 > 78 CR72 > 79 No Rex > 80 LM63 > 81 NS 2-site expanded > 82 IT99 > 83 IT99 > 84 NS 2-site expanded > 85 LM63 > 86 IT99 > > > Troels Emtekær Linnet > > _______________________________________________ > relax (http://www.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://www.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
