Dear Edward. Thank you for reminding me of features which should be implemented.
I will have that in mind for the implementation. I will return to this post, when I have finished the graphs I would like to implement But currently, I have no intention to plot graphs vs offsets. The X-axis I am aiming for is: Per CPMG frequency or spin-lock field strength. Per effective field w_eff. Per theta angle. The first two is interpolating against CPMG frequency or spin-lock field strength. I am still unsure if the last option should be interpolated against spin-lock field strength or spin-lock field offset. Best Troels 2014-07-28 12:01 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > I would suggest maybe the following function names called from > plot_disp_curves(): > > plot_disp_curves_vs_disp_point() > plot_disp_curves_vs_offset() > > The reason would be that the R1rho plots you have created are not > R1rho specific. There is nothing stopping someone from doing this > with CPMG data, by just setting the pi pulse offset to different > nitrogen or carbon frequencies. That is why I have made the offset > structures the same between R1rho and CPMG analyses. The CPMG > analysis has offsets too, and this is one huge advantage CATIA has > compared to all other dispersion software - it handles the offsets > correctly. The offset effect is much weaker in the CPMG experiment > compared to R1rho because of the hard pulses, but it is always present > and cannot be eliminated. > > So if we design the offset parts in the dispersion analysis to work > for both R1rho and CPMG, that would be the best route for future > offset support in the CPMG analysis. Just make the assumption that > CPMG data will be passed through everything you code into the > dispersion analysis - this will result in a cleaner design and allow > for powerful future advancements. This is currently listed as the > first point in the TODO section of the dispersion chapter of the > manual > (http://www.nmr-relax.com/manual/do_dispersion_features_yet_be_implemented.html). > > Cheers, > > Edward > > > > On 26 July 2014 13:34, <[email protected]> wrote: >> Author: tlinnet >> Date: Sat Jul 26 13:34:03 2014 >> New Revision: 24771 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=24771&view=rev >> Log: >> Added functionality to plot R1rho R2 as function of effective field w_eff, >> for the R2eff model. >> >> Also renamed a function, to better reflect is functionality. >> >> The hard-coding of which models to plot, has been removed. >> If the exp-type is R1rho, then the plotting will commence. >> >> sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho >> analysis with R2_eff as function of Omega_eff. >> sr #3138(https://gna.org/support/?3138): Interpolating theta through >> spin-lock offset [Omega], rather than spin-lock field strength [w1]. >> >> Modified: >> branches/r1rho_plotting/specific_analyses/relax_disp/data.py >> >> Modified: branches/r1rho_plotting/specific_analyses/relax_disp/data.py >> URL: >> http://svn.gna.org/viewcvs/relax/branches/r1rho_plotting/specific_analyses/relax_disp/data.py?rev=24771&r1=24770&r2=24771&view=diff >> ============================================================================== >> --- branches/r1rho_plotting/specific_analyses/relax_disp/data.py >> (original) >> +++ branches/r1rho_plotting/specific_analyses/relax_disp/data.py Sat >> Jul 26 13:34:03 2014 >> @@ -1564,8 +1564,9 @@ >> # Plot dispersion curves, extending over number of dispersion points. >> plot_disp_curves_disp(dir=dir, num_points=num_points, extend=extend, >> force=force, proton_mmq_flag=proton_mmq_flag, colour_order=colour_order) >> >> - # For R1rho models, interpolate theta through spin-lock offset rather >> than spin-lock field strength. >> - plot_disp_curves_r1rho(dir=dir, num_points=num_points, extend=extend, >> force=force, proton_mmq_flag=proton_mmq_flag, colour_order=colour_order) >> + # For R1rho models, interpolate through spin-lock field strength, and >> plot R1rho R2 as function of effective field in rotating frame w_eff. >> + if cdp.exp_type_list == [EXP_TYPE_R1RHO]: >> + plot_disp_curves_r1rho_r2_as_func_of_w_eff(dir=dir, >> num_points=num_points, extend=extend, force=force, >> proton_mmq_flag=proton_mmq_flag, colour_order=colour_order) >> >> # Write a python "grace to PNG/EPS/SVG..." conversion script. >> # Open the file for writing. >> @@ -1703,7 +1704,7 @@ >> add_result_file(type='grace', label='Grace', file=file_path) >> >> >> -def plot_disp_curves_r1rho(dir=None, num_points=None, extend=None, >> force=None, proton_mmq_flag=None, colour_order=None): >> +def plot_disp_curves_r1rho_r2_as_func_of_w_eff(dir=None, num_points=None, >> extend=None, force=None, proton_mmq_flag=None, colour_order=None): >> """Custom 2D Grace plotting function for the dispersion curves, >> interpolating theta through spin-lock offset rather than spin-lock field >> strength. >> >> One file will be created per spin system. >> @@ -1728,9 +1729,6 @@ >> # Skip protons for MMQ data. >> if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H': >> continue >> - # Skip for spin not in model list of r1rho models. >> - elif spin.model not in [MODEL_DPL94, MODEL_TP02, MODEL_TAP03, >> MODEL_MP05, MODEL_NS_R1RHO_2SITE]: >> - continue >> >> # Initialise some data structures. >> data = [] >> @@ -1749,7 +1747,7 @@ >> interpolated_flag = False >> >> # The unique file name. >> - file_name = "theta%s.agr" % spin_id.replace('#', '_').replace(':', >> '_').replace('@', '_') >> + file_name = "r1rho_r2_as_func_of_w_eff%s.agr" % >> spin_id.replace('#', '_').replace(':', '_').replace('@', '_') >> >> if not spin.model in [MODEL_R2EFF]: >> # Interpolate through disp points. >> @@ -1757,6 +1755,16 @@ >> >> else: >> back_calc = None >> + spin_lock_nu1_new = None >> + >> + # Number of spectrometer fields. >> + fields = [None] >> + field_count = 1 >> + if hasattr(cdp, 'spectrometer_frq_count'): >> + fields = cdp.spectrometer_frq_list >> + field_count = cdp.spectrometer_frq_count >> + >> + chemical_shifts, spin_lock_fields_inter, offsets_inter, >> tilt_angles_inter, Delta_omega_inter, w_eff_inter = >> return_offset_data(spins=[spin], spin_ids=[spin_id], >> field_count=field_count, fields=spin_lock_nu1_new) >> >> # Open the file for writing. >> file_path = get_file_path(file_name, dir) >> >> >> _______________________________________________ >> 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 _______________________________________________ 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
