Hi Pat,
yep, you're right - after reading my email, I realised that I had
managed to confuse myself.
Positive values of NC_proc mean the spectrum has been scaled down,
negative values indicate upscaling.
The formula I posted was correct though... :)
And thanks for the tip with the uniform processing!
Horst Joachim Schirra
----------------------------------------------------------------
/ Dr. sc. nat. Horst Joachim Schirra Phone: (+61)7/3346-2021 /
/ Queensland Smart State Fellow Fax: (+61)7/3346-2101 /
/ Institute for Molecular Bioscience /
/ University of Queensland email: [log in to unmask] /
/ Brisbane QLD 4072, Australia http://www.uq.edu.au/~uqhschir /
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----- Original Message -----
From: "Edwards, Pat" <[log in to unmask]>
Date: Thursday, February 14, 2008 7:53 am
Subject: Re: problem with T1 series
> Hi,
>
> I have also encountered this scaling problem, which is indeed
> attributedto different spectra being processed with different
> values of the
> NC_proc parameter. I think the idea is that the Bruker data is stored
> in integer format and has to be scaled to avoid the possibility of
> integer overflow during operations such as phase correction. I
> could be
> wrong, but my understanding is that the parameter works in the
> oppositesense to that described by Horst i.e. NC_proc=2 means that
> the spectrum
> has been scaled DOWN by a factor of 4.
>
> Although it would be nice if this scaling could be accounted for in
> Analysis, in the meantime the problem can be avoided by processing the
> data in Topspin in the following way:
>
> 1. Process all your spectra as normal using xfb (or multixfb)
>
> 2. For each spectrum use the command "dpp" and note the value of
> NC_proc (or alternatively use grep to search the procs files: i.e.
> %grepNC_proc <path to your data>/*/pdata/1/procs)
>
> 3. Note the largest value and then reprocess the data using the
> command"xfb nc_proc <your largest NC_proc value>" i.e. if you had
> three spectra
> for which the values of NC_proc were -3, -1 and 2 your would use "xfb
> nc_proc 2"
>
> 4. Use dpp (or grep) to verify that all spectra now have the same
> valueof NC_proc.
>
> The data can now be used with Analysis.
>
> If you have many spectra to process you can make a modified version of
> the Topspin multixfb au program by replacing the XFB command with
> XCMD("xfb nc_proc <your largest NC_proc value>"). This would need
> updating with the relevant value for NC_proc each time it was used.
> With a few extra lines you can have the program prompt you for this
> parameter.
>
> HTH,
>
> Pat Edwards.
>
> -----Original Message-----
> From: CcpNmr software mailing list [mailto:[log in to unmask]] On
> Behalf Of Wayne Boucher
> Sent: Wednesday, 13 February 2008 9:38 p.m.
> To: [log in to unmask]
> Subject: Re: problem with T1 series
>
>
> Thanks, that's great. (I guess there's probably a Bruker manual that
> probably specifies all of this but I don't have a copy of it.) I'll
> have to see how/if we can work that into the current Analysis. (It
> willdefinitely be in the new version.)
>
> Wayne
>
> On Wed, 13 Feb 2008, Dr Horst Schirra wrote:
>
> > Hi Wayne and Mark,
> >
> > the parameter you want is called NC_proc and will be in the procs
> > processing parameter file for each spectrum.
> >
> > The parameter is a log2 scale, i.e.:
> >
> > NC_proc=2 spectrum has been scaled up by factor of 4
> > NC_proc=1 spectrum has been scaled up by factor of 2
> > NC_proc=0 scaling of spectrum intensity unchanged
> > NC_proc=-1 spectrum has been scaled down by factor of 2 NC_proc=-
> 2
> > spectrum has been scaled down by factor of 4
> >
> > etc.
> >
> > In my relaxation measurements, I typically encounter NC_proc
> values
> > between -2 and -6, just as an indication...
> >
> > The true intensity of any data point is then
> > int_corr= bruker_raw_int * (2 ^ NC_proc)
> >
> > Cheers,
> >
> > Horst Joachim Schirra
> >
> > PS: Can you tell, I had to fiddle with that *a lot*? ;)
> > -------------------------------------------------------------
> ---
> > / Dr. sc. nat. Horst Joachim Schirra Phone: (+61)7/3346-
> 2021 /
> > / Queensland Smart State Fellow Fax: (+61)7/3346-
> 2101 /
> > / Institute for Molecular Bioscience /
> > / University of Queensland email: [log in to unmask] /
> > / Brisbane QLD 4072, Australia http://www.uq.edu.au/~uqhschir /
> > ----------------------------------------------------------------
> >
> >
> >
> > ----- Original Message -----
> > From: Wayne Boucher <[log in to unmask]>
> > Date: Tuesday, February 12, 2008 9:03 pm
> > Subject: Re: problem with T1 series
> > > Hello,
> > >
> > > This is a (relatively recently) known problem. Bruker stores
> > > everythingas ints, not floats, so quite sensibly has a
> multiplier
> > > specified (which we discovered when someone else had a problem
> > > similar to the below). This requires us to add a scale to the C
> > > world, passed down from the Python world, so that the data
> comes
> > > back correctly. For contouring there
> > > is a fix already available (setting the spectrum scale, although
> > > I'll have
> > > to remind myself where this scale is hiding in the Bruker files).
> > > Thisfix is not available for the rates analysis but I guess could
> > > be (if Tim
> > > thinks it makes sense).
> > >
> > > Wayne
> > >
> > > On Tue, 12 Feb 2008, Mark Pfuhl wrote:
> > >
> > > > I tried to extract T1 values from a standard T1 experiment. The
> > > spectrum was
> > > > recorded and processed with Topspin and loaded straight into
> > > analysis. In
> > > > Topspin I got the expected decay but in analysis I have a
> > > sawtooth pattern
> > > > that has no resemblance to the original data.
> > > > The sawtooth appearance suggests that the exponent of the
> > > intensities is
> > > > lost somehow in loading it into analysis.
> > > > Is there something wrong or do I need to load the spectra in a
> > > specific way
> > > > if I want to maintain correct intensities?
> > > > thanks,
> > > > mark
> > > >
> > >
> >
>
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