Subject: Re: [nmr_sparky] distance constraints in 13C-edited spectra
From: Eiso AB
Date: Nov 21 3:25 PM

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--- 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
do you mean CANDID or noeassign perhaps? CYANA can be run in many ways
if Im correct in CANDID the distances are calibrated with the assigned
distances
in the structure from the previous round. so if they are all medium
(what is
your definition of medium by the way?) that probably means that there is
not
much intensity difference in your NOEs. Is that the case? Is the
noe-mixing time
maybe too long?

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?
no

there is no principle difference in how sparky treats C13 or N15
edited noesy spectra, or any other spectra. if theres a difference
is because the spectra are different.

you mentioned daa connectivities; could it be that they are weaker
because the pulssequence uses watergate to suppres the water signal ?
this will also suppress the signals close to the water. in principle you
can correct
for this, be multiplying with the inverse of a sine function whcih goes
through zero at the water.

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?
both CANDID and the noeasssign macro do this automatically.

Eiso


Thanks,

Betty Swanson