Hi, This is not directly calculated as most models don't use omega_eff, but rather the rotating frame tilt angle theta. But support for this would be trivial. Just create a new module called lib.rotating_frame, for example as this is independent of dispersion, and add a function called something like calc_omega_eff(). It would take as arguments the Lamor frequency of the spin (population averaged for exchange processes), the spin-lock offset (or hard pulse offset), and the spin-lock field strength (or pulse strength). Then just use the basic formula (see table 10.2 of the relax manual) to calculate the value per spin, experiment type, and magnetic field.
Alternatively you could modify the specific_analyses.relax_disp.disp_data.return_offset_data() function to calculate the value at the same time it calculates theta. Regards, Edward On 5 March 2014 14:25, Troels Emtekær Linnet <[email protected]> wrote: > Dear Edward. > > Would it be possible to implement the calculation of the parameter: > w_e ? The Omega_eff (Effective field in the rotating frame) ? > http://www.nmr-relax.com/manual/Dispersion_model_summary.html > > As seen in the model DPL94 for 2-site off-resonance fast exchange relaxation. > http://wiki.nmr-relax.com/DPL94 > > This would come in handsome for producing .out files with w_e and for > the wished plotting > feature. > > Best > Troels > > > 2014-02-28 10:33 GMT+01:00 Edward d'Auvergne <[email protected]>: >> Either option would be reasonable. I would suggest, for design and >> implementation simplicity, to choose the option to modify the current >> relax_disp.plot_disp_curves user function. The 2D graphs, whether the >> x-axis is the offset or dispersion point (spin-lock field or nu_CPMG >> value) are all dispersion curves so it would also make more sense for >> the user. You could also look at the grace.write user function for >> inspiration. That user function is far more advanced in its options, >> and you may have interest in replicating some of that functionality as >> well. >> >> Regards, >> >> Edward >> >> >> >> On 28 February 2014 09:54, Troels Emtekær Linnet <[email protected]> >> wrote: >>> Dear Edward. >>> >>> I think I would let you decide where such a function resides best. :-) >>> I simply don't have the insight yet to make such decisions. >>> >>> Best >>> Troels >>> >>> 2014-02-28 9:46 GMT+01:00 Edward d'Auvergne <[email protected]>: >>>> Hi, >>>> >>>> Note that this could be used for CPMG-type data as well, if a user >>>> decides to change the hard pulse offset and run multiple experiments. >>>> It's very unlikely to ever happen, but if added for R1rho, it could >>>> just as easily be added for all data types. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 28 February 2014 09:43, Edward d'Auvergne <[email protected]> wrote: >>>>> Hi, >>>>> >>>>> I always wanted to add this, but never found the time. For an >>>>> implementation, what do you propose? Maybe the >>>>> relax_disp.plot_disp_curves user function could modified to allow the >>>>> X-axis to be specified. Or maybe a new user function based on >>>>> relax_disp.plot_disp_curves could be created. >>>>> >>>>> Regards, >>>>> >>>>> Edward >>>>> >>>>> >>>>> >>>>> On 28 February 2014 09:39, Troels E. Linnet >>>>> <[email protected]> wrote: >>>>>> URL: >>>>>> <http://gna.org/support/?3124> >>>>>> >>>>>> Summary: Grace graphs production for R1rho analysis with >>>>>> R2_eff as function of Omega_eff >>>>>> Project: relax >>>>>> Submitted by: tlinnet >>>>>> Submitted on: Fri 28 Feb 2014 08:39:58 AM UTC >>>>>> Category: None >>>>>> Priority: 5 - Normal >>>>>> Severity: 2 - Minor >>>>>> Status: In Progress >>>>>> Assigned to: tlinnet >>>>>> Originator Email: >>>>>> Open/Closed: Open >>>>>> Discussion Lock: Any >>>>>> Operating System: None >>>>>> >>>>>> _______________________________________________________ >>>>>> >>>>>> Details: >>>>>> >>>>>> For an auto analysis of R1rho, relax produces graphs with >>>>>> >>>>>> R1rho (Relaxation rate in the absence of exchange) [rad/s] as function of >>>>>> Omega_rf (Spin-lock offset, the frequency of the of RF field) [rad/s]. >>>>>> >>>>>> Such graphs can be quite crowded, since for a recorded dataset with for >>>>>> example a variation of 6 spin-lock offset in ppm, the graphs will >>>>>> contain 6 >>>>>> legends. >>>>>> >>>>>> It is suggested to also provide graphs with R2_eff as function of >>>>>> Omega_eff >>>>>> (Effective field in the rotating frame) [rad/s]. >>>>>> >>>>>> An example of such a graph is figure 2 in >>>>>> http://dx.doi.org/10.1021/bi4001062. >>>>>> >>>>>> Both types of figures are attached. >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________________ >>>>>> >>>>>> File Attachments: >>>>>> >>>>>> >>>>>> ------------------------------------------------------- >>>>>> Date: Fri 28 Feb 2014 08:39:58 AM UTC Name: disp_52_N.png Size: 13kB >>>>>> By: >>>>>> tlinnet >>>>>> >>>>>> <http://gna.org/support/download.php?file_id=20207> >>>>>> ------------------------------------------------------- >>>>>> Date: Fri 28 Feb 2014 08:39:58 AM UTC Name: >>>>>> Figure2_Kjaergaard_et_al_2013_Off-resonance_R1rho_relaxation_dispersion_experiments_using_the_DPL_model.png >>>>>> Size: 123kB By: tlinnet >>>>>> >>>>>> <http://gna.org/support/download.php?file_id=20208> >>>>>> >>>>>> _______________________________________________________ >>>>>> >>>>>> 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
