Oh, as the GUI is build on top of the auto-analysis, you just do the same thing. But just with the 'Previous run directory' input element and the 'cluster' button. If you don't use the auto-analysis, that is a completely different story. Then one should look at the auto-analysis relax script auto_analyses/relax_disp.py to see how it is done there, and replicate that.
Regards, Edward On 28 August 2013 13:47, Edward d'Auvergne <[email protected]> wrote: > 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
