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print # Python module imports.from os import getcwd, sep # relax module imports.from data_store import Relax_data_store; ds = Relax_data_store() ############################################# Setup# The pipe names.if not (hasattr(ds, 'pipe_name') and hasattr(ds, 'pipe_bundle') and hasattr(ds, 'pipe_type')): # Set pipe name, bundle and type. ds.pipe_name = 'base pipe' ds.pipe_bundle = 'relax_disp' ds.pipe_type = 'relax_disp' # The data pathif not hasattr(ds, 'data_path'): ds.data_path = getcwd() ############################################ Start setup# Create the data pipe.pipe.create(pipe_name=ds.pipe_name, bundle=ds.pipe_bundle, pipe_type=ds.pipe_type) # Read the spins.spectrum.read_spins(file='1_0_46_0_max_standard.ser', dir=ds.data_path+sep+'peak_lists') # Name the isotope for field strength scaling.spin.isotope(isotope='15N') # Load the experiments settings file.expfile = open(ds.data_path+sep+'exp_parameters_sort.txt', 'r')expfileslines = expfile.readlines()expfile.close() # In MHzyOBS = 81.050# In ppmyCAR = 118.078centerPPM_N15 = yCAR ## Read the chemical shift data.chemical_shift.read(file='1_0_46_0_max_standard.ser', dir=ds.data_path+sep+'peak_lists') ## 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] == "Hello World#": 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. spectrum.read_intensities(file=FNAME, dir=ds.data_path+sep+'peak_lists', spectrum_id=sp_id, int_method='height') # Set the peak intensity errors, as defined as the baseplane RMSD. spectrum.baseplane_rmsd(error=apod_rmsd, spectrum_id=sp_id) # Set the relaxation dispersion experiment type. relax_disp.exp_type(spectrum_id=sp_id, exp_type='R1rho') # Set The spin-lock field strength, nu1, in Hz 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. relax_disp.spin_lock_offset(spectrum_id=sp_id, offset=omega_rf_ppm) # Set the relaxation times (in s). relax_disp.relax_time(spectrum_id=sp_id, time=time_sl) # Set the spectrometer frequency. spectrometer.frequency(id=sp_id, frq=set_sfrq, units='MHz') # Read the R1 data# relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_fitted_values.txt', dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
== Scripts ==
=== 1_setup_r1rho.py ===
<source lang="Python">
</source>
= See also =
[[Category:Tutorials]]
