Hi Troels, Welcome to the relax mailing lists. For now the answer to your question is, unfortunately, no - relax does not officially support relaxation dispersion. The analysis you are running is simple two parameter exponential curve-fitting (http://www.nmr-relax.com/manual/Relaxation_curve_fitting.html). This can be used to find the R2eff or R1rho values if you have measured the full exponential curves, but otherwise you cannot perform a dispersion analysis with this.
This may not be of use for you at the moment, but note that relax has unofficial and incomplete support for dispersion analyses (both CPMG-type and R1rho-type data sets). As relax is open source, there are many NMR spectroscopists who have added code to relax (for example see http://gna.org/project/memberlist.php?group=relax). An initial implementation of the relaxation dispersion analysis was added to a relax branch back in 2009 by Sebastian Morin (http://thread.gmane.org/gmane.science.nmr.relax.devel/1728). But as this was not completed at the time, it was never merged back into the relax main line (the source code where official relax releases come from). I have recently restored the branch to a partially working state and added a graphical interface for the analysis - mainly for my own purposes (http://svn.gna.org/viewcvs/relax/branches/). So at some point in the near future relax will be able to perform the analyses you are interested in. As relax is open source, if you are interested and adventurous enough you are most welcome to help in the development. Even if you do not know how to code, there are many other things which can be done. For example calculating the partial derivatives of the analytic solutions to obtain the gradients and Hessians so that with relax you can have access to far more powerful optimisation algorithms than any of the other dispersion software has access to. Or to create test data whereby the solution is know, or to collect the input and output test data from published results. If you have the subversion version control software installed, you can obtain the code by typing either: $ svn co svn://svn.gna.org/svn/relax/branches/relax-disp or: $ svn co http://svn.gna.org/svn/relax/branches/relax-disp If you are more interested in quickly performing the analysis, I would point you to Dr. Flemming Hansen's CATIA program: http://www.biochem.ucl.ac.uk/hansen/catia/ (the old page is http://pound.med.utoronto.ca/~flemming/catia/). This performs numerically integration of the Bloch-McConnell equations, so not the optimisation of the analytic solutions of Meiboom, Richard-Carver, etc. It is also only for CPMG-type data rather than R1rho, whereas the relax branch will handle both. I hope this information helps. Regards, Edward On 30 April 2013 18:40, Troels Emtekær Linnet <[email protected]> wrote: > 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 > _______________________________________________ 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
