Re: r21920 - /trunk/test_suite/system_tests/relax_disp.pyRe: r21920 - /trunk/test_suite/system_tests/relax_disp.pyHi 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
This is the relax-devel mailing list
On 9 December 2013 17:49, <tlinnet@xxxxxxxxxxxxx> 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."""
>
>
>
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