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httphttps://threadsourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1552mailman/message/36569608/
# {| 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: http40:23 +0100}}| <small><CAED9pY-m5YEjN6KUX88s_yXLpY1BCudUaVvWWmC0U6WkteDnPA@mail.gmail.com></small>|-| [https://threadsourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1800# mailman/message/36569841/ Sean Leo Moro]| {{#time: httpY-m-d H:i:s|Fri, 12 Dec 2014 09:24:51 +0100}}| <small><CAED9pY9eAa7B+pC2+RU_pTXWR14fgtiMAiJdQ7rKw+aY6mALaA@mail.gmail.com></small>|-| [https://threadsourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1787mailman/message/36569491/focus=1788Navratna Vajpai]| {{# Martin Ballaschktime: httpY-m-d H:i:s|Tue, 30 Apr 2013 17:32:21 +0200}}| <small><CAED9pY-JcYpQtVpMe2dQf_iLvztQzVue=2d0mEQzYYnaYcRpnA@mail.gmail.com></small>|-| [https:/thread/sourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1409mailman/message/36569422/focus=1438Shantanu Bhattacharyya]| {{# Shantanu Bhattacharyyatime: Y-m-d H:i:s|Mon, 7 Jan 2013 11: http29:28 +0100}}| <small><CAED9pY_aUzPH0OkZhTc2H=trV1VZ074XMcfT8SHYmKH5Bq6T3Q@mail.gmail.com></small>|-| [https:/thread/sourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1367mailman/message/36569341/focus=1369Mengjun Xue]| {{# Mengjun Xuetime: Y-m-d H:i:s|Thu, 6 Sep 2012 14:14: http19 +0200}}| <small><CAED9pY_R8s31My1w19uh5ss7Cjhh6WJLEs62sUUHsF8SxeEc7g@mail.gmail.com></small>|-| [https://threadsourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1276mailman/message/36569242/focus=1277Fernando Amador]| {{# Fernando Amadortime: Y-m-d H:i:s|Fri, 11 May 2012 09: http34:27 +0200}}| <small><CAED9pY-gtfP__28VpkKgGgRVPAST0S0_Q+Hi94Zre0N=NfVLWg@mail.gmail.com></small>|-| [https:/article/sourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/84mailman/message/36569074/ Dhanasekaran Muthu]| {{# Shantanu Bhattacharyyatime: Y-m-d H:i:s|Tue, 31 Jan 2012 15:45: http22 +0100}}| <small><CAED9pY8UArGMiEf-3_fCjQrBJYPecu+BCGqkqtcSXwSix4e5cQ@mail.gmail.com></small>|-| [https://threadsourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1086mailman/message/36569071/focus=1087Vitaly Vostrikov]| {{# Dhanasekaran Muthutime: Y-m-d H:i:s|Mon, 23 Jan 2012 19:05: http12 +0100}}| <small><CAED9pY8SGxe_rF6RKWmXJwyXjrDhzcPZaw5b-nrkX_Bp+OEYMg@mail.gmail.com></small>|-| [https://threadsourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1152mailman/message/36569049/focus=1153Aldino Viegas]| {{# Vitaly Vostrikovtime: Y-m-d H:i:s|Thu, 22 Sep 2011 10: http32:26 +0200}}| <small><CAED9pY-=rnJ6EjMHAr-YDKOpf8JfG0unLP+JmZD-oOaGXL5Org@mail.gmail.com></small>|-| [https://threadsourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1147mailman/message/36569008/focus=1150Shantanu Bhattacharyya]| {{# Aldino Viegastime: Y-m-d H:i:s|Fri, 27 May 2011 10: http16:48 +0200}}| <small><BANLkTim-PG-kZQGK7Fn+4SLXZ4vO-DxkYw@mail.gmail.com></small>|-| [https:/thread/sourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/1127mailman/message/36568645/focus=1128# Pierre-Yves Savard]| {{#time: Y-m-d H: httpi:s|Thu, 8 Jan 2009 17:41:20 +0100}}| <small><7f080ed10901080841p88137d1v8d04321393f12ab1@mail.gmail.com></small>|-| [https://threadsourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/724mailman/message/36568437/focus=725Keith Constantine]| {{# Keith Constantinetime: Y-m-d H:i:s|Fri, 21 Mar 2008 21:17: http33 +0100}}| <small><7f080ed10803211317k6fb586cfpc305eabbc80a5bf2@mail.gmail.com></small>|-| [https://threadsourceforge.gmane.orgnet/p/nmr-relax/mailman/gmane.science.nmr.-relax-users/thread/7f080ed10705071527r77c2dbe9oa180cd8e0bb8e69a%40domain.user/513hid/focus=517# msg36568252 Clare-Louise Evans]| {{#time: Y-m-d H:i:s|Tue, 8 May 2007 00: http27:59 +0200}}| <small><7f080ed10705071527r77c2dbe9oa180cd8e0bb8e69a@mail.gmail.com></small>|-| [https://threadsourceforge.gmane.orgnet/p/gmane.science.nmr.-relax.user/326mailman/message/36570744/focus=332Hongyan Li]| {{# Hongyan Litime: Y-m-d H:i:s|Thu, 21 Dec 2006 19: http53://thread51 +1100}}| <small><7f080ed10612210053l751e5fd8k96ee6097f0840849@mail.gmanegmail.orgcom></gmane.science.nmr.relax.devel/694/focus=701small>|-|}
# <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 [[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>
→The Question: Fixes for the mailing list links, and conversion into a sortable wikitable.
== Reference ==
== The Question ==
The subject of single field strength data has been discussed numerous times on this mailing list. It is recommended to read previous responses to questions relating to single field strength data, and look the other messages in those threads. You will find these discussions quite informative and highly detailed:
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 relax is capable of performing 100% of the functionality of:
* [[Modelfree4 ]] (with or without the Fast-Modelfree GUI interface)* Dasha[[DASHA]]* [[Tensor2 ]] and* [[DYNAMICS]]
If you play with the optimisation settings you can even find identical results to within machine precision - relax can mimic these other softwares.
In summary:
These steps must be implemented independently of which software you use, as NONE implement the full protocol. Note however that the protocol I developed (in the [d'Auvergne and Gooley, 2007] theory paper and the [d'Auvergne and Gooley, 2008b] paper is fully implemented in relax, however this required multiple field strength data.
I must warn you about using single field strength data. It is now quite difficult to publish a model-free analysis with only single field strength data as most of the field know about the catastrophic analysis failures resulting in large amounts of artificial motion. These failures can also be much more subtle. Many reviewers will ask for such data to be collected as the results cannot not be trusted otherwise. For a model-free analysis, it is almost
essential to collect data at multiple field strengths, otherwise it can be sometimes impossible to distinguish between the anisotropic part of the Brownian tumbling of the molecule and internal motion - specifically due to the NH vectors in secondary structure elements all pointing in a similar direction. I have a much better explanation, as well 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<sub>ex</sub> ]] motions of the [Tjandra et al., 1995] paper.
=== Recommendation ===
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|protocol]] in a relax, [[Modelfree4]], or Dasha [[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[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 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 R<sub>2</sub> data.
