Subject: Re: distance constraints in 13C-edited spectra
From: Tom Goddard
Date: Nov 27 10:20 AM
Previous: 304 Next: 315
Hi Betty,
If your noesy spectra were acquired with a BRUKER spectrometer and
you converted them to UCSF format with the Sparky bruk2ucsf program
then the data values in the UCSF spectra may have odd scaling. In the
BRUKER proc file there is a parameter called NC_proc which indicates a
scale factor for the spectrum values. This parameter is ignored by
the bruk2ucsf program. You might check your proc files for your 15N
and 13C noesy spectra to see if the have the same NC_proc values.
Tom
--- In nmr_sparky@yahoogroups.com , Betty Swanson betswanso@... wrote:
Dear SPARKY and CYANA users,
In SPARKY, for my protein the overall intensities of all cross
peaks in the 13C-edited NOESY spectra are medium or weak. Hence, when
I pool the peak lists from 15N-edited NOESY spectra and 13C-edited
NOESY spectra and run CYANA, the upl file generated after cycle7
contains larger distance constraints (~5.5 angstrom) for specific
cross peaks observed in the 13C-edited spectra. I expect constraints
for those cross peaks to be short (less that 2.5 angstrom) because
they correspond to long range daa connectivity in regions of protein
corresponding to antiparallel betasheet.
Why does SPARKY display relatively weaker peak intensities for
13C-edited NOESY spectra when compared to 15N-edited NOESY spectra? Is
this what you all generally observe? How do you all solve this
problem? I think one method by which this problem can be solved is by
calibrating peak heights separately for 15N-edited and 13C-edited
spectra in CYANA. Can anybody tell me how to do that?
Thanks,
Betty Swanson
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