Hi Edward. Allright, I see your point. :-)
Now I am trying to figure out how to do a clustering analysis. I have added to the wiki: http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved#Inspecting_results_from_the_relax_analysis But I am unsure if I made the clustering correct. It is related to copying of the parameters, and running the minimization with the clustered analysis residues. I looked up in the relax disp manual: "relax disp.parametercopy". (I think the prompt example i wrong?) I can't seem to find a section how to make the minimization to run with a clustering or residues. :-) Thanks :-) Troels Emtekær Linnet 2013/8/28 Edward d'Auvergne <[email protected]>: > 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
