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Model-free analysis single field

356 bytes added, 08:28, 12 December 2014
Added a references section and a first reference.
In summary:
* a) Find an initial diffusion tensor estimate (you can do this in relax by only using model m0). This requires all non-mobile residues and side chain spins to be excluded, and this can be problematic. See the [d'Auvergne and Gooley, 2008b ] paper at http://dx.doi.org/10.1007/s10858-007-9213-3 for an example of the catastrophic failure that this initial estimate can result in. Or the bacteriorhodopsin fragment of Korzhnev et al., 1999 (http://dx.doi.org/10.1023/a:1008356809071) where this complete failure was earlier demonstrated.
* b) Optimise all of the model-free models from m0 to m9. This requires high precision optimisation, for a comparison of all the softwares see the d'Auvergne and Gooley, 2008a model-free optimisation paper at http://dx.doi.org/10.1007/s10858-007-9214-2. Only relax and Dasha implement the full range of model-free models, though the models m6, m7, and m8 cannot be used if only single field strength data is used (m6 is the original 2-time scale motion model of Clore et al., 1990).
Finally, you will probably find it much easier to spend the 7-8 days collecting data at another field strength than to implement the protocol of steps a-i in a relax, Modelfree4, or Dasha script (or via multiple iterations of the GUI programs), as well as study all of the relevant literature to understand all of the types of failures than only occurs with single field strength data. With multiple field strength data you can perform [https://gna.org/users/semor Sebastien Morin's] consistency testing analysis in relax (http://dx.doi.org/10.1007/s10858-009-9381-4 and http://www.nmr-relax.com/manual/Consistency_testing.html). That way you can see if your per-experiment temperature calibration and
per-experiment temperature control techniques have works sufficiently well (http://www.nmr-relax.com/manual/Temperature_control_calibration.html) and if you have used long enough recycle delays. Collecting data at a second field would probably save you significant amounts of time, and has the additional benefit that it would guarantee that the dynamics you see at the end will be real. I cannot emphasize enough how important it is to collect data at multiple fields, most importantly the NOE and R2 data.
 
 
= References =
 
* [*d'Auvergne and Gooley, 2008b] d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. ''J. Biomol. NMR'', '''40'''(2), 121-133. (DOI: [http://dx.doi.org/10.1007/s10858-007-9213-3 10.1007/s10858-007-9213-3]).
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