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
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Re: About model-free analysis