Hi Mengjun, I've been looking for the relevant links as we have discussed this topic a number of times on the relax-users mailing list. One good reference would be to read all the messages sent by myself, Sebastien Morin, Alex Hansen, Michael Marlow, and Gary Thompson in the thread called "CSA & bond length" starting at: http://thread.gmane.org/gmane.science.nmr.relax.user/192 and continued on the relax-devel mailing list at: http://thread.gmane.org/gmane.science.nmr.relax.devel/1115 http://thread.gmane.org/gmane.science.nmr.relax.devel/1116 http://thread.gmane.org/gmane.science.nmr.relax.devel/1119 I'll keep looking for the other threads which discuss this, as this was recently talked about, but I cannot find the messages right now. In summary, for protein backbone NH data you should really use 1.02 Angstrom with -172 ppm CSA. The value of -160 ppm is from solid state studies of peptides and is an underestimation for solution NMR. There is CSA variability but the amount of variability is highly debated. Some of Nico Tjandra's estimates of variability might be on the high side, David Fushman's might be more reasonable. In reality, no one really knows what the real CSA and bond length values are and no one has reliably de-convoluted the internal ps-ns dynamics from these parameters to be able to properly answer this question. Therefore everyone takes the compromise of 1.02 A with roughly -172 ppm (the Hall and Fushman average value). There is another school of thought from the NIH direction of Washington DC which says we should use 1.04 A with -160 ppm. However this will generally shift the order parameters higher and closer to one - causing the optimisation algorithms to have severe problems and failures due to the convolution of the optimisation space that this results in So it is not recommended for a model-free analysis - the removal of zero-point motions concept. As long as you are consistent and know that the order parameters are a relative concept rather than absolute - then you can compare different states. I hope this helps. Regards, Edward P. S. If you do solve this problem reliably, you will probably receive quite a few citations and make a name for yourself. However the NMR field has being trying to solve this unsuccessfully for the last who knows how many decades. So I wouldn't recommend trying unless you have an incredible amount of spare time and don't mind diving into the deepest depths of NMR and physics theory. On 5 September 2012 18:09, <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
Hi, When doing model-free analysis, NH bond length set to 1.02 angstrom normally, but it is a little bit different for different amino acid residue; and also the N chemical shift anisotropy set to say -160 ppm normally, but CSA is changing from residue to residue, How do Relax solve such kind of problem when doing model-free analysis? Regards, Mengjun Xue _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@xxxxxxx 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