Subject: contours/display vs NMRPipe
From: ichsprechedarumichbin
Date: Jan 17, 2007

Next: 334


Hello All,

Apologies if this problem has already been covered, but for some
reason I am able to search through yahoo group archives only
intermitantly today. If it has been answered I would very much
appreciate redirection by message number.

Im using Sparky 3.110 on SuSE 9.3, and while this has been troubling
me for a while, Ive finally just done the apple-to-apple comparison
and believe I must be doing something pretty wrong. Ive converted a
spectrum from NMRPipe to ucsf format via

/usr/local/sparky/bin/pipe2ucsf lp2/test_3D.ft ~/Sparky/UCSF/latest.sparky

When I set the Sparky contour parameters identical to those in NMRDraw
(with the test_3D.ft file selected), and I zoom in on the same set of
peaks in each case, not only do the NMRDraw-displayed peaks look like
they have higher-resolution, the noise level in the Sparky spectrum is
*much* higher. Sparky certainly has much better utility to make the
assignments, but I believe Id have an easier time picking peaks in
NMRDraw.

In other situations I havent really had to worry about the problem,
but my current 64 kDa protein is particularly unforgiving. Ive even
found some instances where I clearly see a peak by NMRDraw, but it
would take
quite a bit of imagination to call it a peak in Sparky. Does anybody
have any idea why the spectra appear so different, and what I might
be doing wrong?

Cheers,
john