Hello all,
Indeed this question is closer of the NMRPipe news group subjects,
but I share here the very friendly and very clear reply from Frank Delaglio
regarding the nmrDaw / nmrPipe process.
All the best,
BR
Eric
-------- Original Message --------
Subject: RE: AMMRL: S/N estimation in nD (n>2).
Date: Wed, 2 Apr 2014 19:15:53 +0000
From: <frank_delaglio_at_agilent.com>
To: <eric.condamine_at_ibs.fr>, <agilent_ammrl_at_general.lists.agilent.com>
Hi All,
About peak picking in nmrDraw: to do 3D peak picking, set "Dimensions:"
to "3" in the "Peak Detect" pop-up, then click "Detect". The current
contour drawing settings will be used as the detection threshold.
About noise estimation: NMRPipe also has its own "black box". In
nmrDraw, the noise estimate of the current 2D plane can be calculated
from the "Draw/Estimate Noise" menu option. The "black box" assumes
that the inner 1/3 of the histogram of intensities belongs mostly to
noise, and figures out what noise level would give rise to such a histogram.
It is also possible to extract statistics of ND spectra and spectral
regions using NMRPipe utilities from the UNIX command line. Some obscure
but still perhaps useful examples are below.
Cheerful Regards,
Frank
#
# Read an entire 2D, show max value and noise estimate:
readROI -ndim 2 -in test.ft2 -out None \
-x X_AXIS 0% 100% -y Y_AXIS 0% 100% \
-silent -vec vMax vEstNoise
#
# Read an entire 3D, show max value and noise estimate:
readROI -ndim 3 -in ft/test%03d.ft3 -out None \
-x X_AXIS 0% 100% -y Y_AXIS 0% 100% -z Z_AXIS 0% 100% \
-silent -vec vMax vEstNoise
#
# Read a particular region of a 2D, show RMS
readROI -ndim 2 -in test.ft2 -out None \
-x X_AXIS 10.5ppm 9.5ppm -y Y_AXIS 124.0ppm 121.0ppm \
-silent -vec vRMS
Available statistics are:
vAvg vEstNoise vMax vMaxAbs vMaxLoc vMedian vMin vMinAbs vMinLoc vRMS
vStdDev vSum
*From:*Eric Condamine [mailto:eric.condamine_at_ibs.fr]
*Sent:* Wednesday, April 02, 2014 4:10 AM
*To:* Agilent AMMRL distribution
*Subject:* AMMRL: S/N estimation in nD (n>2).
Hello all,
Just to know your feedback on the S/N determination:
- With nmrDraw, we get a fairly accurate determination of S/N on 2D
spectrum (by determining the noise with SDev and peak heigh). However, I
did not succeed with a 3D spectrum (it seems that peak picking is only
done in the first plane. May be I do a mishandling).
- With sparky It is posible to obtain a S/N estimation (LT) but it is a
pretty black box and I do not like this.
For plans coming from nD (n>2) what are the method(s) you use and what
is the estimated accuracy of the method(s) ?
Thanks in advance,
Eric.
--
Eric Condamine <http://fr.linkedin.com/pub/eric-condamine/27/529/290>
Institut de Biologie Structurale
Groupe Flexibilite et Dynamique des Proteines par RMN
UMR 5075 CNRS/CEA/UJF
CEA/GRENBOLE/BATIMENT IBS2
CAMPUS EPN
6 rue jules Horowitz
38000 Grenoble
Tel: (00 33) 4 5742 8642
Fax: (00 33) 4 76 50 18 90
e-mail:eric.condamine_at_ibs.fr
Received on Wed Apr 02 2014 - 21:38:53 MST