Hi, I'm not suggesting implementing anything additional, just to keep in mind that it will be used not only for R1rho but also CPMG. That way the code you design will be automatically more flexible and powerful, without any extra features. It will also let the next person expand on your advances.
Cheers, Edward On 28 July 2014 12:12, Troels Emtekær Linnet <[email protected]> wrote: > 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
