RMSD

Reference

Art Palmer's 1991 JACS paper

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.

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.

Notes

The error is equal to the baseplane RMSD times the number of 2D spectra points in the box.

Peak shifts

Be aware of peak shifts, due to temperature

References

Palmer et al JACS (1991) 113(12):4371
Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance carbon-13 heteronuclear NMR spectroscopy
Arthur G. Palmer III, Mark Rance , Peter E. Wright
J. Am. Chem. Soc., 1991, 113 (12), pp 4371–4380, DOI: 10.1021/ja00012a001, Publication Date: June 1991

Farrow et al Biochemistry (1994) 33:5984
Backbone Dynamics of a Free and a Phosphopeptide-Complexed Src Homology 2 Domain Studied by 15N NMR Relaxation
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
Biochemistry, 1994, 33 (19), pp 5984–6003, DOI: 10.1021/bi00185a040 Publication Date: May 1994