Hi Edward. The error for r2eff seems twice as high, while i0_err are almost identical.
Best Troels R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0. r2eff=8.646/8.646 r2eff_err=0.0348/0.0692 i0=202664.191/202664.191 i0_err=699.6443/712.4201 R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2. r2eff=10.377/10.377 r2eff_err=0.0403/0.0810 i0=206049.558/206049.558 i0_err=776.4215/782.1833 R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5. r2eff=10.506/10.506 r2eff_err=0.0440/0.0853 i0=202586.332/202586.332 i0_err=763.9678/758.7052 R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0. r2eff=10.903/10.903 r2eff_err=0.0476/0.0922 i0=203455.021/203455.021 i0_err=837.8779/828.7280 R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1. r2eff=10.684/10.684 r2eff_err=0.0446/0.0853 i0=218670.412/218670.412 i0_err=850.0210/830.9558 R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5. r2eff=10.501/10.501 r2eff_err=0.0371/0.0742 i0=206502.512/206502.512 i0_err=794.0523/772.9843 R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1. r2eff=11.118/11.118 r2eff_err=0.0413/0.0827 i0=216447.241/216447.241 i0_err=784.6562/788.0384 R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5. r2eff=7.866/7.866 r2eff_err=0.0347/0.0695 i0=211869.715/211869.715 i0_err=749.2776/763.6930 R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1. r2eff=9.259/9.259 r2eff_err=0.0331/0.0661 i0=217703.151/217703.151 i0_err=682.2137/685.5838 R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5. r2eff=9.565/9.565 r2eff_err=0.0373/0.0745 i0=211988.939/211988.939 i0_err=839.0313/827.0373 R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5. r2eff=3.240/3.240 r2eff_err=0.0127/0.0253 i0=214417.382/214417.382 i0_err=595.8865/613.4378 R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1. r2eff=5.084/5.084 r2eff_err=0.0177/0.0352 i0=226358.691/226358.691 i0_err=660.5314/655.7670 R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1. r2eff=2.208/2.208 r2eff_err=0.0091/0.0178 i0=228620.553/228620.553 i0_err=564.8353/560.0873 R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1. r2eff=1.711/1.711 r2eff_err=0.0077/0.0155 i0=224087.486/224087.486 i0_err=539.4300/546.4217 2014-08-25 16:35 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi, > > The errors from the covariance matrix estimate, via > scipy.optimize.leastsq() should be similar or even identical to the > Monte Carlo simulation errors, not double. Is this still the case? > > Regards, > > Edward > > On 25 August 2014 01:32, <[email protected]> wrote: >> Author: tlinnet >> Date: Mon Aug 25 01:32:13 2014 >> New Revision: 25238 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=25238&view=rev >> Log: >> Modified systemtest Relax_disp.test_estimate_r2eff. >> >> This is to compare against errors simulated with 2000 MC. >> >> The paramaters are comparable, but not equal. >> Mostly, it seems that the errors from scipy.optimize.leastsq, are twice as >> high than the Monte Carlo simulations. >> This affect model fitting, and the calculated chi2 value. >> >> Left column is 2000 Monte Carlo, right column is scipy.optimize.leastsq. >> >> Optimised parameters for spin: 52V @N >> Model: No Rex >> Parameter: r1 Value: 1.46138806 - 1.46328102 >> Parameter: r2 Value: 11.48392438 - 11.48040934 >> Parameter: chi2 Value: 848.42015672 - 3363.95829122 >> >> Model: DPL94 >> Parameter: r1 Value: 1.44845743 - 1.45019848 >> Parameter: r2 Value: 10.15688373 - 10.16304892 >> Parameter: phi_ex Value: 0.07599563 - 0.07561937 >> Parameter: kex Value: 4460.43707304 - 4419.03906628 >> Parameter: chi2 Value: 179.47041255 - 710.24767560 >> >> Model: TP02 >> Parameter: r1 Value: 1.54354392 - 1.54352369 >> Parameter: r2 Value: 9.72654895 - 9.72772727 >> Parameter: pA Value: 0.88827039 - 0.88807488 >> Parameter: dw Value: 1.08875836 - 1.08765645 >> Parameter: kex Value: 4921.28597928 - 4904.70134941 >> Parameter: chi2 Value: 29.33882481 - 114.47142772 >> >> Model: TAP03 >> Parameter: r1 Value: 1.54356410 - 1.54354368 >> Parameter: r2 Value: 9.72641885 - 9.72759371 >> Parameter: pA Value: 0.88828925 - 0.88809317 >> Parameter: dw Value: 1.08837248 - 1.08726695 >> Parameter: kex Value: 4926.42974479 - 4909.86896567 >> Parameter: chi2 Value: 29.29050624 - 114.27987534 >> >> Model: MP05 >> Parameter: r1 Value: 1.54356415 - 1.54354372 >> Parameter: r2 Value: 9.72641730 - 9.72759220 >> Parameter: pA Value: 0.88828927 - 0.88809322 >> Parameter: dw Value: 1.08837250 - 1.08726707 >> Parameter: kex Value: 4926.44228958 - 4909.88128236 >> Parameter: chi2 Value: 29.29054252 - 114.28002272 >> >> Model: NS R1rho 2-site >> Parameter: r1 Value: 1.41359226 - 1.41321968 >> Parameter: r2 Value: 9.34531364 - 9.34602793 >> Parameter: pA Value: 0.94504369 - 0.94496541 >> Parameter: dw Value: 1.56001843 - 1.55833321 >> Parameter: kex Value: 5628.66529504 - 5610.20221435 >> Parameter: chi2 Value: 34.44010458 - 134.14368365 >> >> task #7822(https://gna.org/task/index.php?7822): Implement user function to >> estimate R2eff and associated errors for exponential curve fitting. >> >> Modified: >> trunk/test_suite/system_tests/relax_disp.py >> >> Modified: trunk/test_suite/system_tests/relax_disp.py >> URL: >> http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=25238&r1=25237&r2=25238&view=diff >> ============================================================================== >> --- trunk/test_suite/system_tests/relax_disp.py (original) >> +++ trunk/test_suite/system_tests/relax_disp.py Mon Aug 25 01:32:13 2014 >> @@ -2679,7 +2679,7 @@ >> self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids, read_R1=False) >> >> # The dispersion models. >> - MODELS = [MODEL_NOREX, MODEL_DPL94] >> + MODELS = [MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, >> MODEL_MP05, MODEL_NS_R1RHO_2SITE] >> >> # The grid search size (the number of increments per dimension). >> GRID_INC = None >> @@ -2723,6 +2723,9 @@ >> >> # Run the analysis. >> relax_disp.Relax_disp(pipe_name=ds.pipe_name, >> pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS, >> grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL) >> + >> + # Verify the data. >> + self.verify_r1rho_kjaergaard_missing_r1(models=MODELS, >> result_dir_name=result_dir_name, do_assert=False) >> >> >> def test_exp_fit(self): >> @@ -7343,7 +7346,7 @@ >> w_eff_file.close() >> >> >> - def verify_r1rho_kjaergaard_missing_r1(self, models=None, >> result_dir_name=None): >> + def verify_r1rho_kjaergaard_missing_r1(self, models=None, >> result_dir_name=None, do_assert=True): >> """Verification of test_r1rho_kjaergaard_missing_r1.""" >> >> # Check the kex value of residue 52 >> @@ -7382,35 +7385,36 @@ >> # Print value. >> print("%-10s %-6s %-6s %3.8f" % ("Parameter:", >> param, "Value:", value)) >> >> - # Compare values. >> - if spin_id == ':52@N': >> - if param == 'r1': >> - if model == MODEL_NOREX: >> - self.assertAlmostEqual(value, >> 1.46328102) >> - elif model == MODEL_DPL94: >> - self.assertAlmostEqual(value, >> 1.45019848) >> - elif model == MODEL_TP02: >> - self.assertAlmostEqual(value, >> 1.54352369) >> - elif model == MODEL_TAP03: >> - self.assertAlmostEqual(value, >> 1.54354367) >> - elif model == MODEL_MP05: >> - self.assertAlmostEqual(value, >> 1.54354372) >> - elif model == MODEL_NS_R1RHO_2SITE: >> - self.assertAlmostEqual(value, >> 1.41321968, 6) >> - >> - elif param == 'r2': >> - if model == MODEL_NOREX: >> - self.assertAlmostEqual(value, >> 11.48040934) >> - elif model == MODEL_DPL94: >> - self.assertAlmostEqual(value, >> 10.16304887, 6) >> - elif model == MODEL_TP02: >> - self.assertAlmostEqual(value, >> 9.72772726, 6) >> - elif model == MODEL_TAP03: >> - self.assertAlmostEqual(value, >> 9.72759374, 6) >> - elif model == MODEL_MP05: >> - self.assertAlmostEqual(value, >> 9.72759220, 6) >> - elif model == MODEL_NS_R1RHO_2SITE: >> - self.assertAlmostEqual(value, >> 9.34602793, 5) >> + if do_assert: >> + # Compare values. >> + if spin_id == ':52@N': >> + if param == 'r1': >> + if model == MODEL_NOREX: >> + self.assertAlmostEqual(value, >> 1.46328102) >> + elif model == MODEL_DPL94: >> + self.assertAlmostEqual(value, >> 1.45019848) >> + elif model == MODEL_TP02: >> + self.assertAlmostEqual(value, >> 1.54352369) >> + elif model == MODEL_TAP03: >> + self.assertAlmostEqual(value, >> 1.54354367) >> + elif model == MODEL_MP05: >> + self.assertAlmostEqual(value, >> 1.54354372) >> + elif model == MODEL_NS_R1RHO_2SITE: >> + self.assertAlmostEqual(value, >> 1.41321968, 6) >> + >> + elif param == 'r2': >> + if model == MODEL_NOREX: >> + self.assertAlmostEqual(value, >> 11.48040934) >> + elif model == MODEL_DPL94: >> + self.assertAlmostEqual(value, >> 10.16304887, 6) >> + elif model == MODEL_TP02: >> + self.assertAlmostEqual(value, >> 9.72772726, 6) >> + elif model == MODEL_TAP03: >> + self.assertAlmostEqual(value, >> 9.72759374, 6) >> + elif model == MODEL_MP05: >> + self.assertAlmostEqual(value, >> 9.72759220, 6) >> + elif model == MODEL_NS_R1RHO_2SITE: >> + self.assertAlmostEqual(value, >> 9.34602793, 5) >> >> # For all other parameters. >> else: >> @@ -7420,57 +7424,58 @@ >> # Print value. >> print("%-10s %-6s %-6s %3.8f" % ("Parameter:", >> param, "Value:", value)) >> >> - # Compare values. >> - if spin_id == ':52@N': >> - if param == 'phi_ex': >> - if model == MODEL_DPL94: >> - self.assertAlmostEqual(value, >> 0.07561937) >> - >> - elif param == 'pA': >> - if model == MODEL_TP02: >> - self.assertAlmostEqual(value, >> 0.88807487) >> - elif model == MODEL_TAP03: >> - self.assertAlmostEqual(value, >> 0.88809318) >> - elif model == MODEL_MP05: >> - self.assertAlmostEqual(value, >> 0.88809321) >> - elif model == MODEL_NS_R1RHO_2SITE: >> - self.assertAlmostEqual(value, >> 0.94496541, 6) >> - >> - elif param == 'dw': >> - if model == MODEL_TP02: >> - self.assertAlmostEqual(value, >> 1.08765638, 6) >> - elif model == MODEL_TAP03: >> - self.assertAlmostEqual(value, >> 1.08726698, 6) >> - elif model == MODEL_MP05: >> - self.assertAlmostEqual(value, >> 1.08726706, 6) >> - elif model == MODEL_NS_R1RHO_2SITE: >> - self.assertAlmostEqual(value, >> 1.55833321, 5) >> - >> - elif param == 'kex': >> - if model == MODEL_DPL94: >> - self.assertAlmostEqual(value, >> 4419.03917195, 2) >> - elif model == MODEL_TP02: >> - self.assertAlmostEqual(value, >> 4904.70144883, 3) >> - elif model == MODEL_TAP03: >> - self.assertAlmostEqual(value, >> 4909.86877150, 3) >> - elif model == MODEL_MP05: >> - self.assertAlmostEqual(value, >> 4909.88110195, 3) >> - elif model == MODEL_NS_R1RHO_2SITE: >> - self.assertAlmostEqual(value, >> 5610.20221435, 2) >> - >> - elif param == 'chi2': >> - if model == MODEL_NOREX: >> - self.assertAlmostEqual(value, >> 3363.95829122) >> - elif model == MODEL_DPL94: >> - self.assertAlmostEqual(value, >> 710.24767560) >> - elif model == MODEL_TP02: >> - self.assertAlmostEqual(value, >> 114.47142772) >> - elif model == MODEL_TAP03: >> - self.assertAlmostEqual(value, >> 114.27987534) >> - elif model == MODEL_MP05: >> - self.assertAlmostEqual(value, >> 114.28002272) >> - elif model == MODEL_NS_R1RHO_2SITE: >> - self.assertAlmostEqual(value, >> 134.14368365) >> + if do_assert: >> + # Compare values. >> + if spin_id == ':52@N': >> + if param == 'phi_ex': >> + if model == MODEL_DPL94: >> + self.assertAlmostEqual(value, >> 0.07561937) >> + >> + elif param == 'pA': >> + if model == MODEL_TP02: >> + self.assertAlmostEqual(value, >> 0.88807487) >> + elif model == MODEL_TAP03: >> + self.assertAlmostEqual(value, >> 0.88809318) >> + elif model == MODEL_MP05: >> + self.assertAlmostEqual(value, >> 0.88809321) >> + elif model == MODEL_NS_R1RHO_2SITE: >> + self.assertAlmostEqual(value, >> 0.94496541, 6) >> + >> + elif param == 'dw': >> + if model == MODEL_TP02: >> + self.assertAlmostEqual(value, >> 1.08765638, 6) >> + elif model == MODEL_TAP03: >> + self.assertAlmostEqual(value, >> 1.08726698, 6) >> + elif model == MODEL_MP05: >> + self.assertAlmostEqual(value, >> 1.08726706, 6) >> + elif model == MODEL_NS_R1RHO_2SITE: >> + self.assertAlmostEqual(value, >> 1.55833321, 5) >> + >> + elif param == 'kex': >> + if model == MODEL_DPL94: >> + self.assertAlmostEqual(value, >> 4419.03917195, 2) >> + elif model == MODEL_TP02: >> + self.assertAlmostEqual(value, >> 4904.70144883, 3) >> + elif model == MODEL_TAP03: >> + self.assertAlmostEqual(value, >> 4909.86877150, 3) >> + elif model == MODEL_MP05: >> + self.assertAlmostEqual(value, >> 4909.88110195, 3) >> + elif model == MODEL_NS_R1RHO_2SITE: >> + self.assertAlmostEqual(value, >> 5610.20221435, 2) >> + >> + elif param == 'chi2': >> + if model == MODEL_NOREX: >> + self.assertAlmostEqual(value, >> 3363.95829122) >> + elif model == MODEL_DPL94: >> + self.assertAlmostEqual(value, >> 710.24767560) >> + elif model == MODEL_TP02: >> + self.assertAlmostEqual(value, >> 114.47142772) >> + elif model == MODEL_TAP03: >> + self.assertAlmostEqual(value, >> 114.27987534) >> + elif model == MODEL_MP05: >> + self.assertAlmostEqual(value, >> 114.28002272) >> + elif model == MODEL_NS_R1RHO_2SITE: >> + self.assertAlmostEqual(value, >> 134.14368365) >> >> >> # Print the final pipe. >> @@ -7524,7 +7529,7 @@ >> >> # Assign the split of the line. >> mol_name, res_num, res_name, spin_num, spin_name, val, >> sd_error = line_split >> - print mol_name, res_num, res_name, spin_num, spin_name, >> val, sd_error >> + print(mol_name, res_num, res_name, spin_num, spin_name, >> val, sd_error) >> >> if res_num == '52': >> # Assert that the value is not None. >> >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-commits 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-commits > > _______________________________________________ > 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
