Dear Madam or Sir,

I am trying to use Sparky to measure the heteronuclear NOE ratio.
However, when I import the .ucsf data into sparky, I notice an
inconsistency in the height values of the peaks between different
spectra. I am using bruk2ucsf to convert processed Bruker files into
Sparky, and the peak heights I measure in TopSpin and Sparky do not
match. It seems that the data are scaled during the conversion to
sparky format.
could you give me some details about how bruk2ucsf rescales the peak
heights?

Thank you in advance for your time,
Nikolas Sgourakis

Hi Nikolas,

The problem is that a Bruker parameter file indicates a scale factor
for the data in parameter NC_proc that Sparkys bruk2ucsf ignores, but
Brukers own software applies when using the data. That parameter
must have different values for your different spectra. I dont know
why. There is no Sparky utility to scale the data values. So you
need to fix the problem with the Bruker software by getting it to use
the same NC_proc value for each of the spectra, so that the data
values in the actual 2rr files are scaled the same.

Theres a note about this problem in the Sparky requested features list:

bruk2ucsf NC_proc parameter (Markus Seifert)
NC_proc in proc file indicates scaling of data values. Need to apply
this to compare intensities from different spectra.


http://www.cgl.ucsf.edu/home/sparky/requested-features.html#brukerscale

I dont know if the NC_proc parameter is in the acqu*s or proc*s
parameter files.

http://www.cgl.ucsf.edu/home/sparky/manual/files.html#ConvertBruker

Good luck,

Tom

Dear Tom,

Thank you very much for your reply. I have solved the problem by
reading the NC_proc value from the bruker files and modify accordingly
by reprocessing in Bruker:

xfb NC_proc=[value]

I have one more question:

Can sparky give an estimate of the background noise of a spectrum
(perhaps as the rms of the background signal) ? I have noticed the rh
command for the processing of relaxation data produces errors but it
is unclear in the manual how the original noise in the spectrum is
estimated. I am trying to measure noise in hnNOE spectra, so this
information would be very helpful.

Thanks again,
Nik