Hi Edward and relax user list! Thanks a lot for useful comments, advice and links for further reading. I'll continue using, arguing with, and hugging the relax software and because of this it is likely I'll return with more questions.
Best regards Johan > On 4 Dec 2021, at 11:23, Edward d'Auvergne <[email protected]> wrote: > > On Mon, 29 Nov 2021 at 12:15, Johan Wallerstein <[email protected]> > wrote: >> Thanks a lot for many clarifications and useful comments in your answer. >> Much appreciated. Most important for me, the value.write() command solved >> the main issues, now I easily get all s2, te, and chi2. > > No problems! > > >> One, quite small, question mark remains. How do I get an estimate of the >> global correlation time (tm)? > > For this, there is no *.write() user function. You can however use > the diffusion_tensor.display() user function and output to a log file > or read the values directly from screen. > > >> I use one magnetic field only, I have read in many comments on the mail list >> that one field is suboptimal, for many reasons, I’m aware of this, but since >> my protein (in)stability doesn’t admit more NMR-time, one field I hope is >> better than no field! > > The best resource for this is: > > http://wiki.nmr-relax.com/Model-free_analysis_single_field > > In summary, if you have lots of internal motions, internal motions > that are directionally clustered due to the 3D structure, multi-domain > motions, or a slightly anisotropic system, you must study and be > prepared for the motions to be absorbed into the diffusion tensor and > hidden. > > >> So based on my analysis, >> Protein ca 400 residues >> one field 800 MHz, >> T1-, T2- and NOE-data for most residues >> is there any neat way to get an estimate of the global correlation time (or >> diffusion tensor) from relax? > > See the above link. The local tm models from relax are essential for > your study. > > >> Or is this only possible using two or more fields? > > As the wiki article states, single field strength is possible. But > you must know your demons if you go down that route ;) > > >> (I could get a rough estimate of tm from other software, e.g. David >> Fushman’s Matlab-based ROTDIF.) > > relax will give you the exact value (but the single strength data > might mean that the diffusion tensor absorbs some of your internal > motions or 3D anisotropy). And it will give you the all important > local tm values for comparison. > > >> I apologise if the answer to my question is already clearly posted, I’ve >> searched through quite many posts on the mail list to try to find answers or >> protocols to get a rough estimate of tm, but I haven’t found any. > > The wiki article and all it's links is our best summary and covers > absolutely everything you'll need to know (that the field is currently > aware of). But if you can in any way measure it, multiple field > strength data is superior in every way. I hope this helps. > > Regards, > > Edward > > > _______________________________________________ > nmr-relax-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/nmr-relax-users _______________________________________________ nmr-relax-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/nmr-relax-users
