On 6 June 2016 at 12:37, Petr Padrta <pad...@ncbr.muni.cz> wrote: > On Fri, Jun 03, 2016 at 04:43:18PM +0200, Edward d'Auvergne wrote: >> On 3 June 2016 at 12:08, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >> > Hi Petr, >> > >> > For the new bug report at https://gna.org/bugs/?24675, now looking at >> > the results I can see that this is actually quite a deliberate >> > feature. For reference, I will attach the plots for residues 133 and >> > 134 for the CR2 model as a PDF file to that bug report >> > (disp_CKIRD_133_N.pdf and disp_CKIRD_134_N.pdf). For residue 133, >> > there the blue line can be seen to be the dispersion curve predicted >> > for the missing 600 MHz data. For 134, the green line is the >> > predicted dispersion curve for the 950 MHz data. >> > >> > The R20 values come from the fitting of the single field strength data >> > points, and this value is independent of field strength. So the >> > predicted curves are perfectly correct - they are exactly where they >> > are supposed to be. Assuming the model to be correct, the predicted >> > curves are what the real data should look like. So the curves without >> > measured data are actually quite powerful tools for investigating why >> > the data is missing. They are also useful for investigating how well >> > the model fits to single field strength data. It is also quite easy >> > in Grace to double click on the curve and hide it, if desired. >> > Therefore I think I'll leave the plotting code as it is. >> >> Hi Petr, >> >> Sorry, the R20 values are field strength dependent, but both are fit >> during the optimisation of the dispersion models with missing data. >> This is problematic as one parameter is undefined - the R20 for the >> missing field - and this interferes with optimisation algorithms. The >> undefined R20 value can float around to any value, and this breaks the >> rules that most algorithms absolutely rely on. Hence the solution >> found is unlikely to be the minimum in the optimisation space. I >> would therefore suggest deselecting these spins for now, as the >> results are nonsensical. It might take me a while to update each part >> of relax to detect the missing data for one entire field strength from >> the N fields, and drop back to N-1 fields. This bug might take a >> while to fix! I might have to spend a few days working on that one >> next week. >> >> Regards, >> >> Edward > > Hello Edward, > > Hey, that would be nice if R20 were really independent of B0 ;-) > > Well, the undefined R20 can float to any value but within the bounds (0-200) > so > at least some algorithms should be able to tackle that, Nelder-Mead very > probably amongst them. This seems to be corroborated also by real data. I.e. > when analysing our complete data, (so far) I'm getting sensible results, > comparable to calculating separate residues, of course not counting the R20s > for missing B0s, which sometimes float to 0, at other times go to 200. That's > why I suggested in my bugreports and mails that for the case of leaving all > R20s in, it is probably better to force them to 0. Of course it's even better > to remove missing R20s completely but I expected that to be much more effort.
Hi, The Nelder-Mead simplex tends to have severe problems along these undefined regions (which in this model is across the entire optimisation space). The simplex algorithm can get quite confused. If the global minimum is found, then that is pure luck, as reasonable convergence properties of this algorithm are only guaranteed in a continuous and smooth space. What relax should do is dynamically fall back to N-1 fields for spin systems missing a single whole field of data. But currently the number of fields is defined at the global whole-system level. Most of relax can already currently handle this dynamic algorithm, it is just the packing and unpacking of data for optimisation that would need to be rewritten. Until that is done, I would suggest avoiding those data points, or perform a separate single field strength analysis on them. You may find the same result, but I would not trust relax for these data points yet. Regards, Edward _______________________________________________ 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
