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httphttps://threadsourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1552 == Text ==Questionmailman/message/36569608/

The subject of single field strength data has been discussed numerous times on this mailing list. <br>It is recommended '''Is possible to read previous responses to questions relating use relax to perform a model-free analysis using only relaxation data collected at a single magnetic field strength data, and look the other messages in those threads. <br>You will find these discussions quite informative and highly detailed:?'''

These will have lots The subject of additional informationsingle field strength data has been discussed numerous times on this mailing list. <br>This It is just a selection of possibly recommended to read previous responses to questions relating to single field strength data, and look the most useful other messagesin those threads. You will find these discussions quite informative and highly detailed:

You will soon see that this is a complicated topic{| class="wikitable sortable"|-! Person! Message date! Message ID|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36569855/ Danyun Zeng]| {{#time: Y-m-d H:i:s|Wed, 28 Jan 2015 10:40:23 +0100}}| <small><CAED9pY-m5YEjN6KUX88s_yXLpY1BCudUaVvWWmC0U6WkteDnPA@mail. gmail.com><br/small> Note that |-| [https://sourceforge.net/p/nmr-relax is capable of performing 100/mailman/message/36569841/ Sean Leo Moro]| {{#time: Y-m-d H:i:s|Fri, 12 Dec 2014 09:24:51 +0100}}| <small><CAED9pY9eAa7B+pC2+RU_pTXWR14fgtiMAiJdQ7rKw+aY6mALaA@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36569491/ Navratna Vajpai]| {{#time: Y-m-d H:i:s|Tue, 30 Apr 2013 17:32:21 +0200}}| <small><CAED9pY-JcYpQtVpMe2dQf_iLvztQzVue=2d0mEQzYYnaYcRpnA@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36569422/ Shantanu Bhattacharyya]| {{#time: Y-m-d H:i:s|Mon, 7 Jan 2013 11:29:28 +0100}}| <small><CAED9pY_aUzPH0OkZhTc2H=trV1VZ074XMcfT8SHYmKH5Bq6T3Q@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36569341/ Mengjun Xue]| {{#time: Y-m-d H:i:s|Thu, 6 Sep 2012 14:14:19 +0200}}| <small><CAED9pY_R8s31My1w19uh5ss7Cjhh6WJLEs62sUUHsF8SxeEc7g@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36569242/ Fernando Amador]| {{#time: Y-m-d H:i:s|Fri, 11 May 2012 09:34:27 +0200}}| <small><CAED9pY-gtfP__28VpkKgGgRVPAST0S0_Q+Hi94Zre0N=NfVLWg@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36569074/ Dhanasekaran Muthu]| {{#time: Y-m-d H:i:s|Tue, 31 Jan 2012 15:45:22 +0100}}| <small><CAED9pY8UArGMiEf-3_fCjQrBJYPecu+BCGqkqtcSXwSix4e5cQ@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36569071/ Vitaly Vostrikov]| {{#time: Y-m-d H:i:s|Mon, 23 Jan 2012 19:05:12 +0100}}| <small><CAED9pY8SGxe_rF6RKWmXJwyXjrDhzcPZaw5b-nrkX_Bp+OEYMg@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36569049/ Aldino Viegas]| {{#time: Y-m-d H:i:s|Thu, 22 Sep 2011 10:32:26 +0200}}| <small><CAED9pY-=rnJ6EjMHAr-YDKOpf8JfG0unLP+JmZD-oOaGXL5Org@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36569008/ Shantanu Bhattacharyya]| {{#time: Y-m-d H:i:s|Fri, 27 May 2011 10:16:48 +0200}}| <small><BANLkTim-PG-kZQGK7Fn+4SLXZ4vO-DxkYw@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36568645/ Pierre-Yves Savard]| {{#time: Y-m-d H:i:s|Thu, 8 Jan 2009 17:41:20 +0100}}| <small><7f080ed10901080841p88137d1v8d04321393f12ab1@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/message/36568437/ Keith Constantine]| {{#time: Y-m-d H:i:s|Fri, 21 Mar 2008 21:17:33 +0100}}| <small><7f080ed10803211317k6fb586cfpc305eabbc80a5bf2@mail.gmail.com></small>|-| [https://sourceforge.net/p/nmr-relax/mailman/nmr-relax-users/thread/7f080ed10705071527r77c2dbe9oa180cd8e0bb8e69a% of the functionality of 40domain.hid/#msg36568252 Clare-Louise Evans]* Modelfree4 (with or without the Fast| {{#time: Y-m-Modelfree GUI interface)d H:i:s|Tue, 8 May 2007 00:27:59 +0200}}* Dasha| <small><7f080ed10705071527r77c2dbe9oa180cd8e0bb8e69a@mail.gmail.com></small>* Tensor2 and|-* DYNAMICS| [https://sourceforge.net/p/nmr-relax/mailman/message/36570744/ Hongyan Li]If you play with the optimisation settings you can even find identical results to within machine precision | {{#time: Y-m- relax can mimic these other softwaresd H:i:s|Thu, 21 Dec 2006 19:53:51 +1100}}| <small><7f080ed10612210053l751e5fd8k96ee6097f0840849@mail.gmail.com></small>|-|}

The key These will have lots of additional information. This is just a selection of possibly the most useful messages. You will soon see that the full analysis protocol this is rather a complicated -many people don't understand this - and topic. Note that these softwares do notimplement relax is capable of performing 100% of the full iterative protocol.<br>Therefore one either have to perform it manually or write a script to perform all functionality of the steps.:

The protocol is described in * [[Modelfree4]] (with or without the relax manual in figure 7.2(http://www.nmrFast-relax.com/manual/diffusion_seeded_paradigm.htmlModelfree GUI interface).* [[DASHA]]* [[Tensor2]] and* [[DYNAMICS]]

In summary:* a) Find an initial diffusion tensor estimate (If you play with the optimisation settings you can do this in relax by only using model m0).<br>This requires all non-mobile residues and side chain spins even find identical results to be excluded, and this can be problematic. Seethe d'Auvergne and Gooley, 2008b paper at http://dx.doi.org/10.1007/s10858within machine precision -007-9213-3 for an example of thecatastrophic failure that this initial estimate relax 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 demonstratedmimic these other softwares.

c) Eliminate failed models (this The key is only available in relax, see that thedfull analysis protocol is rather complicated - many people don'Auvergne t understand this - and Gooley, 2006 model elimination paper athttp://dxthat these softwares do not implement the full iterative protocol.doi.org/10.1007/s10858-006-9007-z) Therefore one either have to perform it manually or write a script to perform all of the steps.

d) Select The protocol is described in the best model-free model for each spin systemrelax manual in figure 7. This againrequires precision modern techniques, with the best being AIC modelselect 2 (see the d'Auvergne and Gooley, 2003 model-free model selectionpaper at http://dxwww.doinmr-relax.orgcom/10.1023manual/A:1021902006114)diffusion_seeded_paradigm. If you areunaware that ANOVA statistics for model selection (hypothesis testingvia chi-squared, F- and t-tests) was abandoned by the field of modelselection over 100 years ago (a field which makes the NMR field lookvery, very smallhtml), then you should really look at that paper.

e) Optimise the global model. This is the diffusion tensor plus themodel-free models for all spin systems. f) Check for convergence (identical chi-squared values to a previousiteration, and not necessarily the last one). If no, then go back tob) and repeat. Note that the chi-squared value can go upsignificantly between iterations, but this is because the model issimplifying itself at a much faster rate by loosing parameters - it'sOccam's razor at work. Again see the d'Auvergne and Gooley, 2008bpaper at httpIn summary://dx.doi.org/10.1007/s10858-007-9213-3 for figuresdemonstrating this. The concept as to what is happening during thiscombined model-free optimisation and model selection algorithm isdescribed in the d'Auvergne and Gooley, 2007 MolBiosyst paper athttp://dx.doi.org/10.1039/b702202f. It can take up to 20 iterationsor more to reach convergence, depending upon the quality of therelaxation data and the 3D structure or the system in study. g) Once steps a-f have been completed for all global models(characterised by the spheroid, prolate spheroid, oblate spheroid, andellipsoid diffusion tensors), then model selection between thedifferent global models needs to be performed.

h<ol style="list-style-type:lower-alpha"> <li>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 for an example of the catastrophic failure that this initial estimate can result in. Or the bacteriorhodopsin fragment of [Orekhov et al., 1999] where this complete failure was earlier demonstrated.</li> <li>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. 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]).</li> <li>Eliminate failed models (this is only available in relax). See the [d'Auvergne and Gooley, 2006] model elimination paper.</li> <li>Select the best model-free model for each spin system. This again requires precision modern techniques, with the best being AIC model select (see the [d'Auvergne and Gooley, 2003] model-free model selection paper). If you are unaware that ANOVA statistics for model selection (hypothesis testing via chi-squared, F- and t-tests) was abandoned by the field of model selection over 100 years ago (a field which makes the NMR field look very, very small), then you should really look at that paper.</li> <li>Optimise the global model. This is the diffusion tensor plus the model-free models for all spin systems.</li> <li>Check for convergence (identical chi-squared values to a previous iteration, and not necessarily the last one). If no, then go back to b) and repeat. Note that the chi-squared value can go up significantly between iterations, but this is because the model is simplifying itself at a much faster rate by loosing parameters - it's Occam's razor at work. Again see the [d'Auvergne and Gooley, 2008b] paper for figures demonstrating this. The concept as to what is happening during this combined model-free optimisation and model selection algorithm is described in the [d'Auvergne and Gooley, 2007] paper. It can take up to 20 iterations or more to reach convergence, depending upon the quality of the relaxation data and the 3D structure or the system in study.</li> <li>Once steps a-f have been completed for all global models (characterised by the spheroid, prolate spheroid, oblate spheroid, and ellipsoid diffusion tensors), then model selection between the different global models needs to be performed.</li> <li>Monte Carlo simulations for error analysis must be performed at the end.</li> <li>Elimination of failed Monte Carlo simulations is essential for keeping the errors to reasonable values for certain spin systems. This is also a relax-only feature (see the [d'Auvergne and Gooley, 2007] model elimination paper).</li></ol>

i) Elimination These steps must be implemented independently of failed Monte Carlo simulations is essential forkeeping which software you use, as NONE implement the errors to reasonable values for certain spin systemsfull protocol.This is also a relax-only feature Note however that the protocol I developed (see in the [d'Auvergne and Gooley, 2007model elimination ] theory paper athttp://dx.doi.org/10.1007/s10858-006-9007-z)and the [d'Auvergne and Gooley, 2008b] paper is fully implemented in relax, however this required multiple field strength data.

These steps must be implemented independently of which software youuse, as NONE implement the full protocol. Note however that theprotocol I developed (in the d'Auvergne and Gooley, 2007 theory paperat http://dx.doi.org/10.1039/b702202f and the d'Auvergne and Gooley,2008b paper at http://dx.doi.org/10.1007/s10858-007-9213-3) is fullyimplemented in relax, however this required multiple field strengthdata. This is a rather large script located at'''auto_anlayses/dauvergne_protocol.py'''. This protocol is used by theGUI. So one option would be to copy this'''auto_anlayses/dauvergne_protocol.py ''' script and modify it for thefigure 7.2 protocol.

*** Note *** I must warn you about using single field strength data. It is now quite difficult to publish a model-free analysis with onlysingle field strength data as most of the field know about thecatastrophic analysis failures resulting in large amounts ofartificial motion. These failures can also be much more subtle. Manyreviewers will ask for such data to be collected as the results cannotnot be trusted otherwise. For a model-free analysis, it is almostessential to collect data at multiple field strengths, otherwise itcan be sometimes impossible to distinguish between the anisotropicpart of the Brownian tumbling of the molecule and internal motion -specifically due to the NH vectors in secondary structure elements allpointing in a similar direction. I have a much better explanation, aswell as citations to all the relevant literature in:[d'Auvergne and Gooley, 2007]. In this paper, you will see reviewed both the artificial nanosecond motions of the [Schurr et al., 1994] paper and the artifical [[Rex|R_ex]] motions of the [Tjandra et al., 1995] paper.

In this paperFinally, you will see reviewed both probably find it much easier to spend the 7-8 days collecting data at another field strength than to implement the artificial nanosecondmotions [[#Protocol|protocol]] in a relax, [[Modelfree4]], or [[DASHA]] script (or via multiple iterations of the Schurr 1994 paper and GUI programs), as well as study all of the artifical Rex motions relevant literature to understand all of thetypes 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[Morin and Gagné, 2009] (see http://www.nmr-relax.com/manual/Consistency_testing.html). That way you can see if your per-experiment temperature calibration andTjandra 1995 paperper-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.

Regards*[*Clore et al.,1990] {{#lst:Citations|Clore90}}* [*d'Auvergne and Gooley, 2003] {{#lst:Citations|dAuvergneGooley03}}* [*d'Auvergne and Gooley, 2006] {{#lst:Citations|dAuvergneGooley06}}* [*d'Auvergne and Gooley, 2007] {{#lst:Citations|dAuvergneGooley07}}* [*d'Auvergne and Gooley, 2008a] {{#lst:Citations|dAuvergneGooley08a}}* [*d'Auvergne and Gooley, 2008b] {{#lst:Citations|dAuvergneGooley08b}}* [*Morin and Gagné, 2009] {{#lst:Citations|MorinGagné09}}* [*Orekhov et al., 1999] {{#lst:Citations|Orekhov99}}* [*Schurr et al., 1994] {{#lst:Citations|Schurr94}}* [*Tjandra et al., 1995] {{#lst:Citations|Tjandra95}}<HarvardReferences />