Hi Troels, When looking at this data and analysis, remember that I have not implemented Dmitry Korzhnev's "correction" for constant time R1rho data. I don't know if that was used in the original publication for your data. More details are given in the 'To do' section of the manual (I only recently added this info). I also don't know what the rest of the field think of his correction and how it applies to later models from the Palmer group.
Regards, Edward On 9 December 2013 17:49, <[email protected]> wrote: > Author: tlinnet > Date: Mon Dec 9 17:49:49 2013 > New Revision: 21920 > > URL: http://svn.gna.org/viewcvs/relax?rev=21920&view=rev > Log: > Added system test for the analysis of optimisation of the Kjaergaard et al., > 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' > model. > > Work in progress for Support Request #3083, > (https://gna.org/support/index.php?3083) - Addition of Data-set for R1rho > analysis. > > 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=21920&r1=21919&r2=21920&view=diff > ============================================================================== > --- trunk/test_suite/system_tests/relax_disp.py (original) > +++ trunk/test_suite/system_tests/relax_disp.py Mon Dec 9 17:49:49 2013 > @@ -2450,6 +2450,137 @@ > self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2, > 0.030959849811015544, 3) > > > + def test_r1rho_kjaergaard(self): > + """Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho > relaxation dispersion experiments using the 'DPL' model. > + > + This uses the data from Kjaergaard's paper at U{DOI: > 10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}. > + > + """ > + > + # The path to the data files. > + data_path = status.install_path + > sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' > + > + # Set pipe name, bundle and type. > + pipe_name = 'base pipe' > + pipe_bundle = 'relax_disp' > + pipe_type= 'relax_disp' > + > + # Create the data pipe. > + self.interpreter.pipe.create(pipe_name=pipe_name, > bundle=pipe_bundle, pipe_type=pipe_type) > + > + # Read the spins. > + > self.interpreter.spectrum.read_spins(file='1_0_46_0_max_standard.ser', > dir=data_path+sep+'peak_lists') > + > + # Test some of the sequence. > + self.assertEqual(len(cdp.mol), 1) > + self.assertEqual(cdp.mol[0].name, None) > + self.assertEqual(len(cdp.mol[0].res), 48) > + > + # Name the isotope for field strength scaling. > + self.interpreter.spin.isotope(isotope='15N') > + > + # Set number of experiments to be used. > + NR_exp = -1 > + > + # Load the experiments settings file. > + expfile = open(data_path+sep+'exp_parameters_sort.txt','r') > + expfileslines = expfile.readlines()[:NR_exp] > + expfile.close() > + > + # In MHz > + yOBS = 81.050 > + # In ppm > + yCAR = 118.078 > + centerPPM_N15 = yCAR > + > + ## Read the chemical shift data. > + > self.interpreter.chemical_shift.read(file='1_0_46_0_max_standard.ser', > dir=data_path+sep+'peak_lists') > + > + # Test the chemical shift data. > + cs = [122.223, 122.162, 114.250, 125.852, 118.626, 117.449, 119.999, > 122.610, 118.602, 118.291, 115.393, > + 121.288, 117.448, 116.378, 116.316, 117.263, 122.211, 118.748, > 118.103, 119.421, 119.317, 119.386, 117.279, > + 122.103, 120.038, 116.698, 111.811, 118.639, 118.285, 121.318, > 117.770, 119.948, 119.759, 118.314, 118.160, > + 121.442, 118.714, 113.080, 125.706, 119.183, 120.966, 122.361, > 126.675, 117.069, 120.875, 109.372, 119.811, 126.048] > + > + i = 0 > + for spin, spin_id in spin_loop(return_id=True): > + print spin.name, spin.num, spin_id, spin.chemical_shift, cs[i] > + # Check the chemical shift. > + self.assertEqual(spin.chemical_shift, cs[i]) > + > + # Increment the index. > + i += 1 > + > + # The lock power to field, has been found in an calibration > experiment. > + spin_lock_field_strengths_Hz = {'35': 431.0, '39': 651.2, '41': > 800.5, '43': 984.0, '46': 1341.11, '48': 1648.5} > + > + # Apply spectra settings. > + for i in range(len(expfileslines)): > + line=expfileslines[i] > + if line[0] == "#": > + continue > + else: > + # DIRN I deltadof2 dpwr2slock ncyc trim ss sfrq > + DIRN = line.split()[0] > + I = int(line.split()[1]) > + deltadof2 = line.split()[2] > + dpwr2slock = line.split()[3] > + ncyc = int(line.split()[4]) > + trim = float(line.split()[5]) > + ss = int(line.split()[6]) > + set_sfrq = float(line.split()[7]) > + apod_rmsd = float(line.split()[8]) > + spin_lock_field_strength = > spin_lock_field_strengths_Hz[dpwr2slock] > + > + # Calculate spin_lock time > + time_sl = 2*ncyc*trim > + > + # Define file name for peak list. > + FNAME = "%s_%s_%s_%s_max_standard.ser"%(I, deltadof2, > dpwr2slock, ncyc) > + sp_id = "%s_%s_%s_%s"%(I, deltadof2, dpwr2slock, ncyc) > + > + # Load the peak intensities. > + self.interpreter.spectrum.read_intensities(file=FNAME, > dir=data_path+sep+'peak_lists', spectrum_id=sp_id, int_method='height') > + > + # Set the peak intensity errors, as defined as the baseplane > RMSD. > + self.interpreter.spectrum.baseplane_rmsd(error=apod_rmsd, > spectrum_id=sp_id) > + > + # Set the relaxation dispersion experiment type. > + self.interpreter.relax_disp.exp_type(spectrum_id=sp_id, > exp_type='R1rho') > + > + # Set The spin-lock field strength, nu1, in Hz > + > self.interpreter.relax_disp.spin_lock_field(spectrum_id=sp_id, > field=spin_lock_field_strength) > + > + # Calculating the spin-lock offset in ppm, from offsets > values provided in Hz. > + frq_N15_Hz = yOBS * 1E6 > + offset_ppm_N15 = float(deltadof2) / frq_N15_Hz * 1E6 > + omega_rf_ppm = centerPPM_N15 + offset_ppm_N15 > + > + # Set The spin-lock offset, omega_rf, in ppm. > + > self.interpreter.relax_disp.spin_lock_offset(spectrum_id=sp_id, > offset=omega_rf_ppm) > + > + # Set the relaxation times (in s). > + self.interpreter.relax_fit.relax_time(time=time_sl, > spectrum_id=sp_id) > + > + # Set the spectrometer frequency. > + self.interpreter.spectrometer.frequency(id=sp_id, > frq=set_sfrq, units='MHz') > + > + # The dispersion models. > + MODELS = ['R2eff', 'No Rex', 'DPL94'] > + > + # The grid search size (the number of increments per dimension). > + GRID_INC = 4 > + > + # The number of Monte Carlo simulations to be used for error > analysis at the end of the analysis. > + MC_NUM = 3 > + > + # Model selection technique. > + MODSEL = 'AIC' > + > + # Run the analysis. > + relax_disp.Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, > results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, > modsel=MODSEL) > + > + > def test_r2eff_read(self): > """Test the operation of the relax_disp.r2eff_read user function.""" > > > > _______________________________________________ > 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
