Ok. I will raise Errors until this feature is implemented.
But it should be straight forward to extend the code from now on. Best Troels 2014-07-31 14:04 GMT+02:00 Edward d'Auvergne <[email protected]>: > If we design everything to work for both CPMG and R1rho, then this > will be incredibly easy to implement. The concept of off-resonance > effects in the CPMG is identical as in R1rho, except that the angle > theta is much, much smaller as we are using hard pulses whereas the > spin lock pulse is much weaker. But the idea is identical between the > two. Therefore to implement it only requires a new numeric model from > Flemming's papers, and the user function for inputting the CPMG pi > pulse power and length to convert to w_eff, theta, etc. The same > infrastructure for the R1rho is then used for this off-resonance > handling CPMG model. > > Regards, > > Edward > > > > On 31 July 2014 12:40, Edward d'Auvergne <[email protected]> wrote: >> Hi, >> >> The reference for this is the CATIA software and Flemming Hansen's >> papers on the subject. This will require a new numeric model - the >> one that CATIA uses. And a new user function for specifying the >> details about the hard pi pulse. The current set of models in relax >> will not handle this. This effect can be significant the closer the >> peaks are to the top and bottom edge of the spectrum (assuming the >> hard pi pulse is near the centre of the spectrum), and even more for >> folded peaks. So glycines are most affected. No other software >> handles this yet, only CATIA. But the plan is to add this in the >> future, which is why it is on the to do list >> (http://www.nmr-relax.com/manual/do_dispersion_features_yet_be_implemented.html). >> >> Regards, >> >> Edward >> >> >> On 31 July 2014 12:17, Troels Emtekær Linnet <[email protected]> wrote: >>> Hi Edward. >>> >>> For this to work, could all CPMG models be expanded? >>> >>> Or how is CPMG models influenced by offset? >>> >>> I guess that special offset CPMG models needs to be implemented? >>> >>> 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
