I think I got it now. :-) Here is now my entry how to do the clustering. http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved#Execute_a_clustering_analysis
There is a bug, which prevent it do be done through the GUI, so only the script works. Best Troels Troels Emtekær Linnet 2013/8/28 Edward d'Auvergne <[email protected]>: > Hi, > > The original pipe actually is called something like 'origin - > relax_disp (Wed Aug 28 16:54:13 2013)'. But you should save the > program state yourself prior to the first GUI analysis. Otherwise the > steps are more complicated from the perspective of the students you > are targeting and the logic is more difficult to follow. Also, the > 'Previous run directory' should match the 'Results directory' from the > previous analysis, and not the "NS 2-site expanded" directory. > > Regards, > > Edward > > > > On 28 August 2013 16:43, Troels Emtekær Linnet <[email protected]> wrote: >> 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
