Re: Adding value.write of theta/w_eff to auto-analysis of relax_didp for R1rho experiments. -- March 12, 2014 - 18:09

Hi Edward.

I am looking to calculate
R2_eff = spin.r20 + (phi_ex * k_ ex )/ (k_ex^2+w_e^2 )
R2_eff = (spin.r2eff - spin.ri_data['R1'] *cos(t)**2) / sin(t) **2

As also noted here
http://thread.gmane.org/gmane.science.nmr.relax.devel/5164

Best
Troels

Troels Emtekær Linnet


2014-03-12 17:45 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> Hi Troels,
>
> The R2_eff value stored in spin.r2eff should already contain the R1
> contribution.  Have a look lib.dispersion.dpl94.  The spin.r2eff value
> is equivalent to the back_calc value.  If you would like to isolate
> the pure R1rho contribution, that would be the spin.r20 parameter.  So
> maybe if you use grace.write with the theta parameter on the X-axis
> and r20 on the Y-axis, this will already automatically work.
>
> Regards,
>
> Edward
>
>
> On 12 March 2014 14:32, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
> > The two issues I am trying to resolve, is to make graphs of:
> >
> > R2_eff as function of Omega_eff.
> > https://gna.org/support/?3124
> >
> > where
> > R2,eff = (R1rho - R1*cos(t)*2) / sin(t) *2
> >
> > I would implement another function to calculate this, as:
> > R1rho : spin.r2eff
> > R1 is the loaded R1 values : spin.ri_data
> > and theta I just calculated.
> >
> > And plot R1rho as function of theta (and looping over offset).
> >
> > I think I will now try to implement the relax_disp.write_disp_curves
> > for R1rho as function of theta.
> >
> > best
> > Troels
> >
> >
> > Troels Emtekær Linnet
> >
> >
> > 2014-03-12 13:54 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > Hi,
> > >
> > > What does the output look like?  Could you copy and paste an example?
> > > I'm guessing the relax code is now fully functional so that these
> > > files can be created.  If so, then creating these files in the
> > > auto-analysis would not be a problem.  What is the plan for the
> > > relax_disp.write_disp_curves user function?
> > >
> > > Regards,
> > >
> > > Edward
> > >
> > >
> > >
> > > On 12 March 2014 13:43, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
> > > > Hi Edward.
> > > >
> > > > I would like to add the custom to write out:
> > > > value.write(param='theta', file='theta.out')
> > > > value.write(param='w_eff', file='w_eff.out')
> > > >
> > > > For those models who are in the list
> > > > MODEL_LIST_R1RHO_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_M61, MODEL_M61B,
> > > > MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE,
> > > > MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]
> > > > """The list of the R2eff model together with all dispersion models
> > > > specifically for R1rho-type experiments."""
> > > >
> > > > In the relax_disp auto-analysis, in write_results()
> > > >
> > > > I was thinking to add:
> > > >
> > > >         # The theta/w_eff parameter.
> > > >         if model in MODEL_LIST_R1RHO_FULL:
> > > >             self.interpreter.value.write(param='theta', file='theta.out',
> > > > dir=path, force=True)
> > > >             self.interpreter.value.write(param='w_eff', file='w_eff.out',
> > > > dir=path, force=True)
> > > >
> > > > Do you support this?
> > > >
> > > > Best
> > > > Troels
> > > >
> > > >
> > > >
> > > > Troels Emtekær Linnet
> > > >
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