Re: [sr #2336] xpk files -- May 25, 2009 - 20:18

Hi,

You should mix peak intensities from NMRView and Noise RMSD in Sparky 
since the values will probably not be scaled the same way, causing 
problems such as what you observed, i.e. errors 4 orders of magnitude 
bigger than values...

To extract the spectrum noise standard deviation, you can use the 
function 'getval' within NMRView...

However, the way the sample script determines the standard deviations to 
use within curve fitting is by the use of replicated spectra (replicated 
delays, with the function "relax_fit.mean_and_error()"). See, for 
example, the sample script where delays 0.0176, 0.0704, 0.1584 and 
0.1936 are all replicated.

Do you have replicated spectra ? If yes, this is the approach you might 
want to choose.

Regards,


Séb  :)



Elio Cino wrote:
> Thanks for the help. It now works! However, I am having trouble with 
> the error values. The SDev for the noise in the spectra from nmrview 
> is 0.0. However, if I use the RMSD function in sparky to get noise 
> values, the errors on the plotted figures from relax are 4 orders of 
> magnitude bigger than the actual data. I know that the data is of 
> fairly high quality. What is the best method for estimating errors for 
> relax? Thanks. 
>
> ----- Original Message -----
> From: Sébastien Morin <sebastien.morin.1@xxxxxxxxx>
> Date: Monday, May 25, 2009 12:30 pm
> Subject: Re: [sr #2336] xpk files
> To: anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx>
> Cc: ecino@xxxxxx, relax-devel@xxxxxxx
>
> > Hi,
> >
> > 1.
> > The function "spectrum.read_intensities()" is not available in
> > relax-1.3.3. It is, however, available in the subversion
> > repository
> > where most up-to-date changes are located.
> >
> > 2.
> > If you use relax-1.3.3, you will have to manually set the peak
> > list
> > format in the function "relax_fit.read()". For example:
> >     relax_fit.read(file='T2_ncyc1.list',
> > format='nmrview',
> > relax_time=0.0176)
> >
> > Let me know if things now work properly.
> >
> > Regards,
> >
> >
> > Séb  :)
> >
> >
> >
> > anonymous wrote:
> > > Follow-up Comment #3, sr #2336 (project relax):
> > >
> > > I am using 1.3.3. I still have no clue how to get it to expect
> > nmrview> opposed to sparky.
> > >
> > >    
> > _______________________________________________________>
> > > Reply to this item at:
> > >
> > >   <http://gna.org/support/?2336>
> > >
> > > _______________________________________________
> > >   Message sent via/by Gna!
> > >   http://gna.org/
> > >
> > >
> > >  
> >
> >
> > --
> > Sébastien Morin
> > PhD Student
> > S. Gagné NMR Laboratory
> > Université Laval & PROTEO
> > Québec, Canada
> >
>
> Elio Cino


--
Sébastien Morin
PhD Student
S. Gagné NMR Laboratory
Université Laval & PROTEO
Québec, Canada