Re: Relax_fit.py problem -- October 15, 2008 - 20:48

I use Sparky frequently but it doesn't support 1D data. I might have to use a
ruler :o


Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:

> On Wed, Oct 15, 2008 at 7:30 PM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> > Okay, so I'll basically just need to get the rms noise (NOT S/N) for my T1
> > and
> > T2 spectra at various fields. I've been using S/N values for the NOE
> > calculations so that explains why those errors seemed so large. I'd like to
> > find a reference for the rms equation which seems to be:
>
> Those would be quite big errors :)
>
>
> > [sqrt(2)]*(baseline noise height)/4
>
> I think:
>
> sigma_h = rmsd(noise),
>
> is sufficient, where sigma_h is the peak height uncertainty and
> rmsd(noise) is the RMSD of the base plane noise.  Tom Goddard added
> the RMSD calculation to Sparky (http://www.cgl.ucsf.edu/home/sparky/)
> - but I've still to thank him for adding that so quickly after I asked
> by giving him a citation.  I don't know if other programs can
> calculate this RMSD value.
>
>
> > Ignoring the stuff with duplicate spectra, it's actually a rather nice
> > situation
> > with only peak height and baseline noise height being the information
> > required
> > for the calculation of NOE, R1, R2, and the propagation of their respective
> > errors. Presumably this would then be enough to begin the model-free
> > analysis
> > in relax?
>
> This would save NMR time and it would be sufficient for a model-free
> analysis if done carefully.  Remember that the RMSD value in the
> random coil region is higher than the empty parts of the spectrum, so
> don't forget to get some estimates by measuring in there.
>
> Regards,
>
> Edward