Hi Edward. I will try to look into it today.
Best Troels 2013/12/9 Edward d'Auvergne <[email protected]> > Hi Troels, > > Note that I will soon release relax 3.1.1 with all of the recent fixes > (possibly tomorrow). This includes the 'NS MMQ 3-site', 'NS MMQ > 3-site linear', 'NS R1rho 3-site', and 'NS R1rho 3-site linear' > dispersion models which are now implemented, tested, and find similar > results to Dmitry Korzhnev's cpmg_fit software. If the test is not > functional by then, I will disable it for the release. It would be > very useful to have fixed though as it looks like variable relaxation > time data (SQ CPMG, MMQ CPMG, or R1rho) will all currently fail in the > auto-analysis. I've had a look and have another hint for you - the > problem is that has_exponential_exp_type() function is not returning > the correct answer ;) > > Regards, > > Edward > > > > On 9 December 2013 18:12, Edward d'Auvergne <[email protected]> wrote: > > 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 <[email protected]> > 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 <[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 > >>> > [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 > >> > >> >
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