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Model-free analysis single field

217 bytes removed, 09:28, 3 March 2014

== Text ==

~~Hi Ivan,~~Question

~~To continue:~~'''I wonder if it is possible to modify the nmr-relax programme so that I can do model-free analysis with data from only one field strength? Alternatively, do you know of any programme (that can be installed on Windows) that can do such analysis?'''

'''On another note, I wonder if it is possible to modify the nmr-relax programme so that I can do model-free analysis with data from only one field strength? Alternatively, do you know of any programme (that can be installed on Windows) that can do such analysis? My work focused mainly on small molecule and ligand-based NMR and I have only just very recently started looking in to protein dynamics so I am still experimentinng different software and data treatment etc. ''' ~~Firstly, the~~ The subject of single field strength data has been discussed numerous times on this mailing list. ~~I would recommend you~~ It is recommended to read myprevious responses to questions relating to single field strengthdata, and look the other messages in those threads. You will findthese discussions quite informative and highly detailed:

#- Martin Ballaschk: http://thread.gmane.org/gmane.science.nmr.relax.user/1409/focus=1438

#- Hongyan Li: http://thread.gmane.org/gmane.science.nmr.relax.devel/694/focus=701

These will have lots of additional information.

This is just a selection of possibly the most useful messages.

You will soon see that this is a complicated topic. Note that relaxis capable of performing 100% of the functionality of * Modelfree4 (with or without the Fast-Modelfree GUI interface), * Dasha, * Tensor2, and* DYNAMICS. If you play with the optimisation settings you can evenfind identical results to within machine precision - relax can mimicthese other softwares.

The key is that the full analysis protocol is rather complicated -

many people don't understand this - and that these softwares do not

implement the full iterative protocol. Therefore ~~you~~ one either have toperform it manually or write a script to perform all of the steps.

The protocol is described in the relax manual in figure 7.2

(http://www.nmr-relax.com/manual/diffusion_seeded_paradigm.html). In~~summary:~~

In summary:* a) Find an initial diffusion tensor estimate (you can do this inrelax by only using model m0). This requires all non-mobile residuesand side chain spins to be excluded, and this can be problematic. Seethe d'Auvergne and Gooley, 2008b paper athttp://dx.doi.org/10.1007/s10858-007-9213-3 for an example of thecatastrophic failure that this initial estimate can result in. Or thebacteriorhodopsin fragment of Korzhnev et al., 1999(http://dx.doi.org/10.1023/a:1008356809071) where this completefailure was earlier demonstrated.

* b) Optimise all of the model-free models from m0 to m9. Thisrequires 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

Tlinnet

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