RMSD

The 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.
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
http://www.cgl.ucsf.edu/home/sparky/manual/extensions.html#RegionRMSD

Whole spectrum
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.

The empty region RMSD is smaller than the random coil region, due to power conservation in the Fourier transform.
You can see this by dropping all the way to the baseplane and carefully looking.
You should measure with boxes near the peaks, and make sure no peaks are in the box.
This estimate is much better than the full spectrum RMSD measures from the other programs.

Peak shifts

Be aware of peak shifts, due to temperature

showApod with NMRPipe

1. http://spin.niddk.nih.gov/NMRPipe/newdocs/ref/
2. http://spin.niddk.nih.gov/NMRPipe/ref/prog/showapod.html
3. http://spin.niddk.nih.gov/NMRPipe/doc/nmrProg/showApod.html
4. https://groups.yahoo.com/neo/groups/nmrpipe/conversations/topics/402
5. https://groups.yahoo.com/neo/groups/nmrpipe/conversations/messages/2003
6. 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

References

• Palmer, 3rd, A. G., Rance, M., and Wright, P. E. (1991). Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance carbon-13 heteronuclear NMR spectroscopy. J. Am. Chem. Soc., 113(12), 4371-4380. (DOI: 10.1021/ja00012a001)

• Farrow, N. A., Muhandiram, R., Singer, A. U., Pascal, S. M., Kay, C. M., Gish, G., Shoelson, S. E., Pawson, T., Forman-Kay, J. D., Kay, L. E. (1994). Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry, 33(19), 5984-6003. (DOI: 10.1021/bi00185a040)

See also

1. Spectrum_error_analysis
2. Message on Yahoo group
3. Jamie Baird-Titus page on Processing RDC Data
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