Hi Mengjun, Sorry for not getting back to you earlier. The papers you mention are:
Oscar Millet and Anthony Mittermaier and David Baker and Lewis E. Kay (2003) The Effects of Mutations on Motions of Side-chains in Protein L Studied by 2H NMR Dynamics and Scalar Couplings. Journal of Molecular Biology, 329, 551-563 (http://dx.doi.org/10.1016/S0022-2836(03)00471-6) Eric Johnson and Walter J. Chazin and Mark Rance (2006) Effects of Calcium Binding on the Side-chain Methyl Dynamics of Calbindin D9k: A 2H NMR Relaxation Study. Journal of Molecular Biology, 357, 1237-1252 (http://dx.doi.org/10.1016/j.jmb.2006.01.031). The key here is that if these papers use the standard model-free theory with no modifications, which I think they do though you need to carefully check this, then this will work fine in relax where the standard theory is implemented. If the theory has been modified and hence is not the original equations, then it might be time to learn some computer programming ;) But if you look at equation (1) of the Rance paper, you will see that they measure 5 quadrupolar relaxation rates. If you have measured these, then you cannot use them in relax yet. There is currently no support in relax for quadrapolar relaxation rates. However it would be relatively easy to add. Note that all of the required infrastructure is in place. The model-free spectral density functions are all located in lib/spectral_densities. Also present are all model-free models, the highest quality optimisation infrastructure, powerful model selection techniques, model elimination infrastructure for failed models, the automated protocol that I came up with for solving the convoluted diffusion tensor vs. internal motion problem (though I don't know if this protocol would work if you only measured Me deuterium relaxation and do not combine it with backbone relaxation), powerfully data visualisation infrastructure, etc. The only work required is: 1) Extending the list of input relaxation data types in the relax_data.read user function. This is trivial - the hard part is deciding what to call these rates. 2) Adding relevant functions to the relax library lib/auto_relaxation/ modules to handle the additional rates. This is where the real work is. 3) Added the quadrupolar coupling constant Q (or e2qQ/h) as a model-free parameter that can be set via the value.set user function (see http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.parameter_object-pysrc.html#Model_free_params.__init__). This requires one line of code. The hardest part would be obtaining published test data. That would only require emailing one of the corresponding authors and explaining what you would like to do, and the data in the Rance paper, especially figure 4 appears to be the best for this. The test data is then turned into a system test - this is a mini-analysis used to check that everything runs as expected. I could do this in ~2 weeks of solid work, but I don't have the time to allocate to such a task. This would also require the gradients and Hessians (1st and 2nd partial derivatives) to be calculated for the relaxation rates: http://www.nmr-relax.com/manual/Ri_theta_gradients.html http://www.nmr-relax.com/manual/Ri_theta_Hessians.html http://www.nmr-relax.com/manual/Ri_prime_theta_gradients.html http://www.nmr-relax.com/manual/Ri_prime_theta_Hessians.html This is rather trivial in Maxima, wxMaxima, Mathematica, or other symbolic algebra systems. However it is so simple that it could be derived by hand in a few minutes. If you would be interested in adding this to relax, you could then mention this in your paper - that you implemented quadrapolar relaxation rates in relax. This could then be added to the reference list in the citations chapter (http://www.nmr-relax.com/manual/Model_free_analysis_references.html) as well as a new section for citations at the start of the model-free chapter (http://www.nmr-relax.com/manual/Model_free_analysis.html) so that people using relax with such rates should then cite your paper. Regards, Edward On 12 June 2014 14:35, <mengjun....@mailbox.tu-berlin.de> wrote: > Hi Edward, > > Thank you so much. I would like to replicate the analysis in the publication > "The Effects of Mutations on Motions of Side-chains in Protein L Studied by > 2H NMR Dynamics and Scalar Couplings" and "Effects of Calcium Binding on the > Side-chain Methyl Dynamics of Calbindin D9k: A 2H NMR Relaxation Study" > > , where models LS2 and LS3 were used for fitting. > > Best regards, > > Mengjun > > > > > > Quoting mengjun....@mailbox.tu-berlin.de: > >> Hi Edward, >> There is some script in Relax software which can be used for analyzing >> side chain dynamics (R1 and R1r of deuterium in CH2D isotopomers)? Thank >> you. >> >> Best regards, >> >> Mengjun > > > > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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-users