Hi, In the tutorial at:
http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved#Inspect_model_selection there is a much better way of accessing the data. A user script should never touch cdp.mol[i].res[j].spin[k]. I, or any relax developer, reserves the right to change this in the future as needed. Instead the spin loop should be used: from pipe_control.mol_res_spin import spin_loop print("%20s %20s" % ("# Spin ID", "Model")) for spin, spin_id in spin_loop(return_id=True, skip_desel=True): print("%20s %20s" % (repr(spin_id), spin.model)) Note the brackets in the print function call. This is essential for Python 3. The other bits will be better formatted for your students. And the spin loop should be easier for them to understand. Accessing cdp.mol[i].res[j].spin[k] should only be done by functions in the pipe_control.mol_res_spin and pipe_control.interatomic modules (or the system tests, as these can be easily changed when the relax data store is redesigned). Regards, Edward On 28 August 2013 13:50, Edward d'Auvergne <[email protected]> wrote: > 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
