Hi, You should base the clustering on the dynamics, not the selected model! For example the 'CR72' analytic model and the 'NS 2-site expanded' numeric model can both describe exactly the same motional process. Clustering is a much more manual operation and it should not be automated. It is based on human logic and is highly subjective. For example it could be decided that one analysis is performed whereby one motional process is assumed, i.e. one kex value for all exchanging spins. Or it could be decided that there are two motional processes, so two clusters are created, each having their own kex. Some spins with bizarre dynamics may be left out as 'free spins' and not used in the cluster. An automated protocol could be devised, but I would assume that that is not your goal. Though if you just want all spins with Rex to be in one cluster, you could just use all spins where spin.model is not set to 'No Rex'.
For the instructions, the sel_residues structure is not very elegant. I would suggest you change this to sel_spins and have it be a list of spin IDs. The major problem is that you are accessing private structures such as spin._res_name. One should never rely on private structures, they may not exist in the next version of relax. There is a option for the spin_loop() generator method to return this information. However you just need spin IDs which are already returned, as the relax_disp.cluster user function only works with spin IDs. The residue level should not be considered. As for the GUI bug, could you submit a bug report with all the details? Cheers, Edward On 28 August 2013 19:11, Troels Emtekær Linnet <[email protected]> wrote: > 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
