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
