Dear Edward, Thank you again for the thorough explanation. You are correct in surmising that I just want to perform the analysis. I did read the text you highlighted, but did not quite understand its implications. Now it is much more clear. We were quite confused by all the different models, and even though we read through most of the papers, evidently we did not understand why the different models were developed, and to what extent have they been applied to “real” biological problems (e.g. novel biological systems instead of model proteins).
Cheers, Chung-ke On Sep 15, 2014, at 9:50 PM, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Hi Chung-ke, > > It is quite confusing with the huge spectrum of relaxation dispersion > models that can be found in the literature covering all different > relaxation dispersion conditions. However you should only use models > when you know that they apply to your system. For the Ishima and > Torchia model (http://wiki.nmr-relax.com/IT99), this has the condition > that pA >> pB, which is quite different to the Carver and Richards > model (http://wiki.nmr-relax.com/CR72) or Nikolai Skrynnikov's > expanded numerical model > (http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded). You really need > to read the primary reference for any model you use. For example in > the Ishima and Torchia paper, you will find the text: > > "Equation 4 predicts values of Rex that agree with those calculated > using Equation 3, within 15%, for all values of δωτex, when p1/p2 < > 0.15." > > Equation 3 is the CR72 model and equation 4 is the IT99 model. > > You should note that the IT99 model is what is known in the field of > mathematical modelling as a 'flexible model'. It is more able to > adapt and fit to the data more than the other models. However that > does not mean that it is better. But it will be chosen more than > non-flexible models using Akaike's Information Criterion (AIC) model > selection. There are more advanced techniques in the field of model > selection which deal with such flexible models, for example ICOMP (the > Information Complexity Criterion). But these are not implemented in > relax for now. For an introduction to model selection in NMR, see my > model-free model selection paper at > http://dx.doi.org/10.1023/A:1021902006114. There are some good > textbook references in there which explain all of this, and why ICOMP > would probably not select the IT99 model. > > However, I would guess that your aim is not to study model selection > or the IT99 model results, but just to perform a dispersion analysis. > The IT99 paper quote above also indicates that this is a very > approximate model, and is probably not what you are looking for. If > this is the case, don't use the IT99 model! Note that the model > selection is provided mainly to see if the dispersion model fits the > data better than the 'No Rex' model - i.e. it is used to judge if the > dispersion process is statistically significant. You cannot compare > the different dispersion models using model selection as the domain of > validity of most models do not match, they are for different > dispersion conditions, and scientific logic always trumps model > selection. > > Anyway, a general rule of thumb is that if you are not sure that a > model is suited for your system, then it probably isn't. You should > also take note of Troels' suggestion of Andy Baldwin's recent model > (http://wiki.nmr-relax.com/B14) which can replace the CR72 model. If > it is all too confusing, then the defaults of simply the 'R2eff', 'No > Rex', 'CR72', and 'NS CPMG 2-site expanded' models should be used. > And maybe you should set the NUMERIC_ONLY value to True so that you > only compare the 'No Rex' and numeric CPMG model. I hope this helps. > > Regards, > > Edward > > > > On 15 September 2014 04:56, Chung-ke Chang <chun...@ibms.sinica.edu.tw> wrote: >> Dear all, >> >> I’ve been tearing my hair out trying to figure out how to choose relaxation >> dispersion models for a particular protein. I’ve ran into a case where many >> residues are fit to the ‘IT99’ model, but did not fit to the ’NS CPMG 2-site >> expanded’ model (relax doesn’t even bother to show the Chi2 and AIC in the >> log file). If I understand correctly, the ’NS CPMG 2-site expanded’ model is >> an exact numerical solution based on the original Bloch-McConnell equations, >> whereas ‘IT99’ is an analytical approximation. I would expect that whatever >> can be fit with the ‘IT99’ model should also be able to fit to the ’NS CPMG >> 2-site expanded’ model since they seem to share the same restrictions (pA > >> pB). Or am I missing something? >> >> Cheers, >> >> Chung-ke >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-users mailing list >> relax-users@gna.org >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-users _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
