Hi,
This is a strange failure! The auto-analysis should not be running
the calc user function for this. That is the problem, you cannot run
the calc user function for non-constant relaxation time experiments.
The error message is the standard one to tell the user that. The
grid_search and minimise user functions should be used instead (maybe
the error message can be modified to clarify this and include this
info). But it is the auto-analysis that is running this. So the
problem is there. relax can of course handle variable relaxation
times for any dispersion data type.
Regards,
Edward
On 9 December 2013 18:02, Troels Emtekær Linnet <tlin...@nmr-relax.com> wrote:
> 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 <edw...@nmr-relax.com>
>>
>> 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, <tlin...@nmr-relax.com> 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
>> > relax-comm...@gna.org
>> >
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>> > reminder, or change your subscription options,
>> > visit the list information page at
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>>
>> _______________________________________________
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>>
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>
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