Re: Help with settings script for R1rho analysis. -- October 22, 2013 - 13:46

Hi,

Ok, I made the assumption that deltadof2 was not the spin-lock offset
(in ppm) but rather the spin-lock field strength (in Hz).  The ppm
values as printed out from the r1rho_1_ini.py script are far too low
for 15N.  They should be in the range of 100-120 ppm!  I.e. around the
15N chemical shifts.  They can be much higher and much lower for
off-resonance data, but having many at an offset of 0.0 ppm seems a
little strange.

Regards,

Edward

On 22 October 2013 13:18, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
> Hi Edward.
>
> Thanks for looking at this.
>
> The offset for N15 spinlock is given in Hz as parameter deltadof2
> for our pulse sequence.
>
> So I guess that this conversions should be appropriate:
> omega_rf_ppm = float(deltadof2) / (set_sfrq * 1E6) * 1E6
>
> where set_sfrq=799.7773991 is the spectrometer frequency.
>
> Best
> Troels
>
>
> 2013/10/22 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
> > Hi,
> >
> > In the relax prompt, have a look at:
> >
> > relax> help(relax_disp.spin_lock_offset)
> >
> > The unit you need is ppm.  You can find this number directly from the
> > Bruker acqus or Varian procpar files.  It is the ppm offset of the
> > spin-lock pulse which is manually set by the person recording for each
> > spectrum.  You may need to go to the original pulse sequence to know
> > which pulse this is.  It will be a fixed value for each spectrum
> > collected and you can use that value directly.  The calculations in
> > your scripts seem far to complicated and it looks like the internal
> > conversions performed within relax.  You should never need
> > gyromagnetic ratios, factors of pi, etc.  If you do, you should
> > probably go back to the original experiments and pull out the correct
> > offset number in ppm for each spectrum.  I hope this helps.
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> >
> > On 22 October 2013 10:46, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>
> > wrote:
> > > Hi Edward.
> > >
> > > I wonder if would have time to look at the settings script in:
> > > test_suite/shared_data/dispersion/Kjaergaard_et_al_2013
> > >
> > > It is the scripts:
> > > r1rho_1_ini.py
> > > r1rho_3_spectra_settings.py
> > >
> > > In r1rho, I am unsure if I do the correct conversion from Hz to ppm for
> > > omega_rf.
> > >
> > > Again, if there is hidden radian units?
> > >
> > > It is when I set:
> > > relax_disp.spin_lock_offset
> > >
> > > And I wonder, how to start modifying, so R1 rates can be read per
> > > spectra?
> > >
> > > Best
> > > Troels
> > >
> > >
> > >
> > >
> > >
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