The [https://en.wikipedia.org/wiki/Root-mean-square_deviation Root Mean Squared Deviation] (RMSD) of the baseplane noise in a spectrum.
== Software to use ==
SPARKY. In the extension menu.
In F1 mode, draw boxes in the empty regions for all spectra. You have a different error estimate for each spectrum, which relax handles.
It is a good idea to use the Sparky '''rm''' function to get the RMSD of the spectrum as a maximal noise estimate in several areas free of peaks. <br>
If there are peaks which may be in noisier regions (eg near the water line) it can be a good idea to give those peaks separate errors by measuring the RMSD near those peaks seperately.
=== Reference ===
For a region <br>
http://www.cgl.ucsf.edu/home/sparky/manual/extensions.html#RegionRMSD
Whole spectrum <br>
http://www.cgl.ucsf.edu/home/sparky/manual/views.html#Noise
== Notes ==
The error is equal to the baseplane RMSD times the number of 2D spectra points in the box.
== Reference ==
Do this for PEAK HIGHTS determination.
This estimate is much better than the full spectrum RMSD measures from the other programs.
== Software to use ==
SPARKY. In the extension menu.
In F1 mode== Peak shifts ==Be aware of peak shifts, due to temperature == showApod with NMRPipe ==# http://spin.niddk.nih.gov/NMRPipe/newdocs/ref/# http://spin.niddk.nih.gov/NMRPipe/ref/prog/showapod.html# http://spin.niddk.nih.gov/NMRPipe/doc/nmrProg/showApod.html# http://hincklab.uthscsa.edu/~ahinck/html/soft_packs/nmrpipe/nmrDraw.html# https://groups.yahoo.com/neo/groups/nmrpipe/conversations/topics/402# https://groups.yahoo.com/neo/groups/nmrpipe/conversations/messages/2003# https://groups.yahoo.com/neo/groups/nmrpipe/conversations/messages/2382 showApod test.ft2 | grep "REMARK Automated Noise Std Dev in Processed Data:" | awk '{print $9} ' This will print two numbers, first is noise estimate for the spectrum, second is noise estimate for the time-domain ... try it without the "-noverb" option to see more info. showApod -in test.ft2 -noverb [https://groups.yahoo.com/neo/groups/nmrpipe/conversations/topics/402 Post by Frank Delaglio, Oct 29, 2009]<source lang="text">Hi George, A section of an earlier post about noise estimation is below. The noise estimation is supposed to estimate the standard deviationin the baseline of the spectrum, draw boxes i.e. the areas of the spectrumwithout substantial signal. It assumes: 1. The noise level in the spectrum is uniform 2. The noise has a Gaussian distribution, or roughly so. 3. Most of the spectrum is "empty regions for all spectra", i.e. free ofsubstantial signal. So, if the noise estimation is successful, it will give valuessimilar to those that you would find if you manually identifya baseline region and take its standard deviation. You have Along these lines, you can imagine that by looking at the histogramof intensities in a different error signal-free region, you could also estimate for each itsstandard deviation. As the post below says, some noise estimation tools use the entirespectral data set at once. However, this is NOT the same assimply taking the standard deviation of the entire spectrumat once, since the entire spectrumincludes both signal ANDbaseline. Instead, the noise estimation techniques attempt to separate thecontributions from "signal" and "baseline". In our case,we assume that most points are baseline points, such that ifwe build a histogram of intensities, most of the valuescorresponding to small intensities come from the baselinerather than from the signals. This means that to a firstapproximation, the part of the histogram describing the smallestintensities can be used to characterize the baseline. In practice, this noise estimation technique works betterwhen we perform many independent noise estimates on vectorsfrom the data, rather than perform one noise estimate usingall the data at once. This is because individual vectors froma 2D or 3D dataset are more likely to contain a substantial fractionof baseline points, and in fact many individual vectors will consistentirely of baseline, in which relax handlescase the histogram method will beat its most effective. Hope this explanation helps ... big fd From an earlier post about noise estimation: ---The noise estimation details used by autoFit.tcl were recentlyimproved ... if you search the text of the script, the olderversion will use the function "vEstNoise", and the newerversion will use the function "estSpecNoise".
== Notes ==The error basic mechanism of noise detection is equal to the baseplane RMSD times same in bothcases; a histogram of the number data intensities is analyzed, underthe assumption that most of 2D spectra the points in the boxspectrum arein the baseline, so that the innermost part of the histogramis due primarily to baseline noise. IF we assume that thebaseline noise is normally distributed, we can use the histogramto estimate the standard deviation of the noise.<br>
== Peak shifts ==The older "vEstNoise" implementation analyzed an entire spectralBe aware region at once to form a single noise estimate. In the case of peak shifts2D/3Ddata, the newer "estSpecNoise" forms separate noise estimates for individualvectors from the data, due to temperatureand uses the median.---</source>
== References ==
[http://pubs.acs.org/doi/abs/10.1021/ja00012a001 Palmer et al JACS (1991) 113(12):4371] <br>
''Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance carbon-13 heteronuclear NMR spectroscopy''<br>
Arthur G. Palmer III, Mark Rance , Peter E. Wright <br>
J. Am. Chem. Soc., 1991, 113 (12), pp 4371–4380, DOI: 10.1021/ja00012a001, Publication Date: June 1991
[http* {{#lst://pubs.acs.org/doi/abs/10.1021/bi00185a040 Farrow et al Biochemistry (1994) 33:5984] <br>Citations|Palmer91}}''Backbone Dynamics of a Free and a Phosphopeptide-Complexed Src Homology 2 Domain Studied by 15N NMR Relaxation''<br>Neil A. Farrow , Ranjith Muhandiram , Alex U. Singer , Steven M. Pascal , Cyril M. Kay , Gerry Gish , Steven E. Shoelson , Tony Pawson , Julie D. Forman-Kay , Lewis E. Kay <br>Biochemistry, 1994, 33 (19), pp 5984–6003, DOI: 10.1021/bi00185a040 Publication Date* {{#lst: May 1994Citations|Farrow94}}
== See also ==
# [[Spectrum_error_analysis]]
# [http://tech.groups.yahoo.com/group/nmr_sparky/message/102 Message on Yahoo group]
# [https://sites.google.com/site/jamiebairdtitus/analyzingusingrdcdata Jamie Baird-Titus page on Processing RDC Data]
# [https://groups.yahoo.com/neo/groups/nmrpipe/conversations/messages/2382 ][[Category:Analysistechniques]]