Hi Edward. I tried to generate sherekhan output, but since I have time_T2 of 0.04 and 0.06, for the two fields, I cannot generate the input files for ShereKhan.
My problem origins from that I would like to compare results from Igor Pro script. Yet, another software solution. I now got the expected pA values of 0.97 if I did a cluster of two residues. If I do an initial Grid inc of 21, use relax_disp.set_grid_r20_from_min_r2eff(force=False) I get this. :10@N GRID r2600=20.28 r2500=18.48 dw=1.0 pA=0.900 kex=2000.80 chi2=28.28 spin_id=:10@N resi=10 resn=G :10@N 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 :10@N Clust r2600=18.43 r2500=16.98 dw=2.7 pA=0.972 kex=3831.77 chi2=48.79 spin_id=:10@N resi=10 resn=G :11@N GRID r2600=19.54 r2500=17.96 dw=1.0 pA=0.825 kex=3500.65 chi2=47.22 spin_id=:11@N resi=11 resn=D :11@N MIN r2600=14.98 r2500=15.08 dw=1.6 pA=0.760 kex=6687.15 chi2=18.36 spin_id=:11@N resi=11 resn=D :11@N Clust r2600=18.19 r2500=17.31 dw=2.7 pA=0.972 kex=3831.77 chi2=48.79 spin_id=:11@N resi=11 resn=D Ideally, I would like to cluster 68 residues. But as you can see, if several of my residues start out with dw/pA far from the Clustered result, this minimisation takes hilarious long time. I am very soon ready to send last fixes. 2014-04-29 19:19 GMT+02:00 Edward d'Auvergne <[email protected]>: > 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
