Hi Edward. Allright.
So, I should create a copy from the "base pipe" to a new pipe "cluster". The "base pipe" contains the spectra intensities, but nothing else. And the I cluster atoms in this pipe. Then start an auto analysis. Point to "NS 2-site expanded" in "Precious run directory". And then select model "R2eff", "No Rex" and "NS 2-site expanded" Or... :-) Best Troels Troels Emtekær Linnet 2013/8/28 Edward d'Auvergne <[email protected]>: > No problems! For the clustered analysis, you need to start again from > the start. You do not load the final state, this will likely be fatal > for the clustered analysis (actually, I don't know what will happen, > but don't do it). The auto-analysis is designed to take the pre-run > directory name and load the results files for each model itself (not > the state file). Each results file will be loaded into a temporary > data pipe and the initial parameter values copied from that. You > should not load a state or results file yourself for the clustered > analysis. > > Regards, > > Edward > > > P. S. One exception is that you could have a state file with all data > loaded but prior to clicking the 'execute' button. This is > essentially a short cut to manually loading everything again. > > > > On 28 August 2013 15:36, Troels Emtekær Linnet <[email protected]> wrote: >> Hi Edward. >> >> Thanks for all the tips! >> >> I have a question more. >> >> When I open the final_state.bz2, I have several pipes from the different >> models. >> It is in the pipe "final". >> >> Should I create a new pipe before doing the cluster analysis? >> For example a copy from "final" or from "NS 2-site expanded". >> >> And then do the clustering in that pipe, before an Autoanalysis. >> >> Best >> Troels >> >> >> Troels Emtekær Linnet >> >> >> 2013/8/28 Edward d'Auvergne <[email protected]>: >>> 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
