Re: [sr #2336] xpk files -- May 25, 2009 - 20:26

Sorry, I should have been more specific. I am talking about the errors that we input for the NOE script (noe.py). 

----- Original Message -----
From: Sébastien Morin <sebastien.morin.1@xxxxxxxxx>
Date: Monday, May 25, 2009 2:17 pm
Subject: Re: [sr #2336] xpk files
To: Elio Cino <ecino@xxxxxx>
Cc: anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx>, relax-devel@xxxxxxx

> 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
> 

 Elio Cino