Dear relax users. I am looking into different NMR programs to fit relaxation data for CPMG relaxation dispersion experiments and T1rho.
Essentially, I am looking for programs for which can fit functions, which for example nessy provide: http://home.gna.org/nessy/reference.html The Meiboom equation or Richard-Carver equation Nessy is very buggy, and I am looking for a replacement. I should be able to: R2eff = -1.0/time_T2*log(Intensity/averageZero) ncyc_arr=[28, 0, 4, 32, 60, 2, 10, 16, 8, 20, 50, 18, 40, 6, 12, 0, 24] time_T2 = 0.06 second nu = ncyc_arr[i]/time_T2 R2cpmg_slow: tau_cpmg = 1.0/(4*nu) R2eff = R2+ka*(1.0-sin(Domega*tau_cpmg)/(Domega*tau_cpmg)) I have followed the tutorial in the homepage manual: Can relax analyse these kinds of experiments? Should i provide the: *relax_fit.relax_time(time *to be equal tau_cpmg ? I put in time_T2, even though its wrong. I just wanted to try the program. :-) ---------------------------------------------------------------- """Script for relaxation curve fitting.""" # Create the 'rx' data pipe. pipe.create('rx', 'relax_fit') ## Load the backbone amide 15N spins from a PDB file. pdbfile=False if pdbfile: structure.read_pdb(pdbfile) structure.load_spins(spin_id='@N') else: molecule.create(mol_name='protein', mol_type='protein') residue.create(res_num=2, res_name='VAL') spin.create(res_num=2, spin_name='N') residue.create(res_num=3, res_name='PHE') spin.create(res_num=3, spin_name='N') residue.create(res_num=4, res_name='GLY') spin.create(res_num=4, spin_name='N') residue.create(res_num=5, res_name='ARG') spin.create(res_num=5, spin_name='N') residue.create(res_num=6, res_name='CYS') .... and so on ## Loop over the spectra intensities. Relaxation times should be in seconds. readint=True if readint: spectrum.read_intensities(dir='relax', file='proc_list.txt.0int', spectrum_id='0_0.0', int_method='point sum', heteronuc='N', proton='HN', int_col=3) relax_fit.relax_time(time=0.06, spectrum_id='0_0.0') spectrum.read_intensities(dir='relax', file='proc_list.txt.1int', spectrum_id='1_133.33', int_method='point sum', heteronuc='N', proton='HN', int_col=3) relax_fit.relax_time(time=0.06, spectrum_id='1_133.33') spectrum.read_intensities(dir='relax', file='proc_list.txt.2int', spectrum_id='2_166.67', int_method='point sum', heteronuc='N', proton='HN', int_col=3) relax_fit.relax_time(time=0.06, spectrum_id='2_166.67') spectrum.read_intensities(dir='relax', file='proc_list.txt.3int', spectrum_id='3_333.33', int_method='point sum', heteronuc='N', proton='HN', int_col=3) relax_fit.relax_time(time=0.06, spectrum_id='3_333.33') spectrum.read_intensities(dir='relax', file='proc_list.txt.4int', spectrum_id='4_33.33', int_method='point sum', heteronuc='N', proton='HN', int_col=3) relax_fit.relax_time(time=0.06, spectrum_id='4_33.33') ... and so on # Specify the duplicated spectra. spectrum.replicated(spectrum_ids=['0_0.0', '18_0.0']) spectrum.error_analysis() # Deselect unresolved spins. #deselect.read(file='unresolved', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5) # Set the relaxation curve type. relax_fit.select_model('exp') # Grid search. grid_search(inc=11) # Minimise. minimise('simplex', scaling=False, constraints=False) ## Monte Carlo simulations. monte_carlo.setup(number=10) monte_carlo.create_data() monte_carlo.initial_values() minimise('simplex', scaling=False, constraints=False) monte_carlo.error_analysis() ## Save the relaxation rates. value.write(param='rx', file='rx.out', force=True) ## Save the results. results.write(file='results', force=True) # Save the program state. state.save('rx.save', force=True) Best Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234
_______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users 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-users
