Hi, We should add many more of these details to the dispersion chapter of the relax manual! So for the dispersion auto-analysis, there is the 'pre_run_dir' argument. To use clustering, you just define the cluster with the relax_disp.cluster user function, and then set 'pre_run_dir' to the directory of non-clustered results. That's it. The auto-analysis takes care of the rest.
Regards, Edward On 28 August 2013 13:43, Troels Emtekær Linnet <[email protected]> wrote: > 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
