Hi Troels, Here is the new thread, just to keep things separate and clean. The old thread that this originates from is at http://thread.gmane.org/gmane.science.nmr.relax.devel/5402.
Note that you will always see different results for CPMGFit and all other software when multiple field strength data is involved. The reason is because of a fundamental assumption that that software makes. And that is that R20 is the same for all fields! No other dispersion software makes that assumption as it is know that the all relaxation rates are field strength dependent. So comparing CPMGFit to relax for debugging purposes is not of much use. See the CR72 model in test_suite/shared_data/dispersion/software_comparison for example. Are you sure that the CR72 model is suitable for this data? You could try ShereKhan for a comparison as relax and ShereKhan, from all my testing, produce 100% identical results. Or you could try the "MMQ CR72" model in cpmg_fit from Dmitry Korzhnev. You could also compare the numerical models to the CR72 model all within relax, as these should produce similar results. Regards, Edward On 29 April 2014 17:27, Troels Emtekær Linnet <[email protected]> wrote: > The problem is this: > > For spin 10. After GRID search, and after minimisation. > GRID r2600=20.28 r2500=18.48 dw=1.7 pA=0.917 kex=6667.00 chi2=438.32 > spin_id=:10@N resi=10 resn=G > MIN r2600=19.64 r2500=17.88 dw=0.7 pA=0.500 kex=2665.16 chi2=14.61 > spin_id=:10@N resi=10 resn=G > > I expect that pA should be between 0.95 and 0.99. > > I also tried with cpmgfit: > # Parameter Fitted_Value Fitted_Error Sim_value Sim_error > # R20 13.8014 0.6817 13.7140 > 0.4095 > # papb 0.1134 1.0745 0.1071 > 0.0630 > # dw 0.8920 4.2931 1.2044 > 0.6912 > # kex 7.7524 0.5016 7.7358 > 0.4777 > > From: > relax_trunk/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/README > > 'Full_CPMG' or 'CR72' model parameter conversions. > ================================================== > To convert from the papb parameter: > pA = 1.0 - papb > To obtain dw: > dw = 2.0 * pi * dw > And kex: > kex = kex * 1000 > > So cpmgfit gives pA=0.8866. > > 2014-04-29 16:58 GMT+02:00 Troels Emtekær Linnet <[email protected]>: >> Hi Edward. >> >> I have some serious problems, that relax finds values of pA=0.5 after >> minimisation. >> >> This is in systemtest Relax_disp.test_sod1wt_t25_to_cr72 >> which I am working on. >> >> These two support request, I think is essential for a better R1rho >> inspection: >> #3124 Grace graphs production for R1rho analysis with R2_eff as >> function of Omega_eff >> #3138 Interpolating theta through spin-lock offset [Omega], rather >> than spin-lock field strength [w1] >> >> But I don't have plans to work on them before I get the pA issues solved. >> >> Anyway, maybe relax is in a good current state? >> >> Best >> Troels >> >> >> 2014-04-29 16:38 GMT+02:00 Edward d'Auvergne <[email protected]>: >>> Hi, >>> >>> I'm thinking about soon releasing relax 3.2.0 with all of the bug >>> fixes and the specific analysis API reorganisation and code cleanup. >>> Troels, do you have code lined up or plans which I should take into >>> account for this release? >>> >>> Cheers, >>> >>> Edward >>> >>> _______________________________________________ >>> 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
