Hi Edward. My advisor Kaare Teilum gave these references. ********** 1. Evenäs, J., Malmendal, A. & Akke, M. (2001). Dynamics of the transition between open and closed conformations in a calmodulin C-terminal domain mutant. Structure 9, 185–195 http://dx.doi.org/10.1016/S0969-2126(01)00575-5
2. Kempf, J.G. & Loria, J.P. (2004). Measurement of intermediate exchange phenomena. Methods Mol. Biol. 278, 185–231 http://dx.doi.org/10.1385/1-59259-809-9:185 3. Palmer, A.G. & Massi, F. (2006). Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700–1719 http://dx.doi.org/10.1021/cr0404287 4. Palmer, A.G., Kroenke, C.D. & Loria, J.P. (2001). Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Meth. Enzymol. 339, http://dx.doi.org/10.1016/S0076-6879(01)39315-1 5. Francesca Massi, Michael J. Grey, Arthur G. Palmer III* (2005) Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1ρ relaxation experiments, Protein science, http://dx.doi.org/10.1110/ps.041139505 ************ In general, it is the references to Palmer and Loria, which produces these graphs. Ref [1], Figure 1.b. This is the bell-curves I am after, and should now be possible to obtain, after a correction to the tilt angle calculation. I will return with such a plot. Ref [1], Figure 1.c. This is the graph I am looking for. But no clear "name" for the calculated parameter. Ref [2], Equation 27. Here the calculated value is noted as: R_eff. : Equation 27: R_eff = R1rho / sin^2(theta) - R_1 / tan^2(theta) = R^{0}_2 + R_ex Where R^{0}_2 refers to R1rho_prime as seen at http://wiki.nmr-relax.com/DPL94 Ref [3], Equation 20. Here the calculated value is noted as: R_2: R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) Figure 11+16, would be the reference. Ref [4], Equation 43. R_eff = R1rho / sin^2(theta) - R_1 / tan^2(theta) Ref [5], Material and Methods, page 740. Here the calculated value is noted as: R_2: R_2 = R^{0}_2 + R_ex. Figure 4 would be the wished graphs. **** A little table of conversion then gives Relax equation | Relax store | Articles --------------------------------------------------------------- R1rho' spin.r2 R^{0}_2 or Bar{R}_2 Fitted pars Not stored R_ex R1rho spin.r2eff R1rho R_1 spin.ri_data['R1'] R_1 or Bar{R}_1 The parameter is called R_2 or R_eff in the articles. Since reff is not used in relax, this could be used? A description could be: * The effective rate * The effective transverse relaxation rate constant * The effective relaxation rate constant. Optimal, a function: back_calc_reff in specific_analysis.relax_disp.optimsation would be desired to enable interpolation. Best Troels 2014-03-13 19:45 GMT+01:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > The value of R1rho' + Rex calculated by this script, do you know if it > has a name? It is the on-resonance component of the relaxation and is > equivalent to the data from the 'R1rho - R1' type experiments. But do > you know of a base publication which gives it a name? If this > 'parameter' has a name and is described in the manual, then it could > be implemented as one of the special auto-generated parameters of the > dispersion analysis. As it is, your script would function for all > dispersion models > (http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff). For some > models where the different offsets of each state is important this may > not be technically correct, but it can still be calculated. > > It would be worth getting to the bottom of this. I can see that Art > Palmer sometimes plots just Rex verses w_eff. See > http://dx.doi.org/10.1110/ps.041139505. In that same publication the > parameter is defined as: > > R2 = R1rho' + Rex > > This is in equation 6, and is plotted in figure 4. Maybe we could > just put this equation into the manual, and add R2 as a parameter. > What do you think? > > Regards, > > Edward > > > > > On 13 March 2014 19:05, Troels E. Linnet > <[email protected]> wrote: >> Follow-up Comment #32, sr #3124 (project relax): >> >> Correct graphs of "on-resonance R1rho value with exchange" as function >> "Effective field in rotating frame" finally produced manually with python >> matplotlib and accessing the relax data store. >> >> The graph is attached as: >> matplotlib__52_N_R1rho_R2eff_w_eff.png >> >> This graph corresponds to: >> file #20208: >> Figure2_Kjaergaard_et_al_2013_Off-resonance_R1rho_relaxation_dispersion_experiments_using_the_DPL_model.png >> >> The production of this graph was discussed in: >> http://thread.gmane.org/gmane.science.nmr.relax.devel/5194 >> >> The R1rho_r2eff value is never calculated in relax. >> This value was manually calculated by accessing the data store. >> >> The script to produce such a graph is here: >> http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff >> >> (file #20315) >> _______________________________________________________ >> >> Additional Item Attachment: >> >> File name: matplotlib__52_N_R1rho_R2eff_w_eff.png Size:42 KB >> >> >> _______________________________________________________ >> >> Reply to this item at: >> >> <http://gna.org/support/?3124> >> >> _______________________________________________ >> Message sent via/by Gna! >> http://gna.org/ >> >> >> _______________________________________________ >> 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
