Hi Edward.
The R1rho data is not constant time.
I have only included the models:
MODELS = ['R2eff', 'No Rex', 'DPL94']
I have set it up, to find a solution for analysing R1rho data, where R1
data has not been acquired, but for
different
It actually also fails at the moment, and will probably do for some time.
--------
relax -s Relax_disp.test_r1rho_kjaergaar
relax> calc(verbosity=1)
Traceback (most recent call last):
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/system_tests/relax_disp.py",
line 2581, in test_r1rho_kjaergaard
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)
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py",
line 116, in __init__
self.run()
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py",
line 447, in run
self.interpreter.calc()
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/uf_objects.py",
line 221, in __call__
self._backend(*new_args, **uf_kargs)
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/pipe_control/minimise.py",
line 86, in calc
calculate(verbosity=verbosity)
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py",
line 717, in calculate
self._calculate_r2eff()
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py",
line 182, in _calculate_r2eff
check_exp_type_fixed_time()
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/checks.py",
line 112, in check_exp_type_fixed_time
raise RelaxError("The experiment '%s' is not of the fixed relaxation
time period data type." % exp_type)
RelaxError: RelaxError: The experiment 'R1rho' is not of the fixed
relaxation time period data type.
--------------
Is the R1rho analysis only implemented for fixed time periods?
Best
Troels
2013/12/9 Edward d'Auvergne <[email protected]>
> 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
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> >
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> > visit the list information page at
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>
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