RMSD
The Root Mean Squared Deviation (RMSD) of the baseplane noise in a spectrum.
Contents
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
- 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
- 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
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)
