Difference between revisions of "RMSD"
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== References == | == References == | ||
[http://pubs.acs.org/doi/abs/10.1021/ja00012a001 Palmer et al JACS (1991) 113(12):4371] <br> | [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' | + | ''Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance carbon-13 heteronuclear NMR spectroscopy'' |
| − | |||
== See also == | == See also == | ||
[[Category:Analysis]] | [[Category:Analysis]] | ||
Revision as of 07:01, 24 June 2013
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
