Re: r24771 - /branches/r1rho_plotting/specific_analyses/relax_disp/data.py -- July 31, 2014 - 14:04

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 <edward@xxxxxxxxxxxxx> 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 <tlinnet@xxxxxxxxxxxxx> 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 <edward@xxxxxxxxxxxxx>:
> > > 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,  <tlinnet@xxxxxxxxxxxxx> 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)
> > > >
> > > >
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