Re: About model-free analysis -- September 07, 2012 - 11:15

Hi Mengjun,

Could I ask you to send the message again?  To properly resend a
message, please go to my original message, click on 'reply-to-all',
and then write a new message (copy and paste the text of your missed
message if you wish).

Cheers,

Edward


On 7 September 2012 11:10,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
>
> > Hi Mengjun,
> >
> > Sorry in advance, but the following is the standard pre-composed
> > response to a post not sent to the relax mailing lists and not
> > labelled as private.  If you would like to start a private
> > conversation about relax, please label your message as such.  If you
> > really must start a private exchange, please respond to this message
> > saying so.  If your message was meant to be sent to the relax mailing
> > list, please send the message again.  For this, please copy-and-paste
> > your message, replying to the original (i.e. no forwarding), and
> > making sure that the mailing list is in the CC field by clicking on
> > 'reply-to-all'.
> >
> > Cheers,
> >
> > Edward
> >
> >
> >
> > On 6 September 2012 23:14,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> > > Dear Dr. Edward d'Auvergne,
> > >
> > > Thank you very much for your detailed explanations. There are some bugs
> > > when
> > > I try to import T1 demo.txt from bruker dynamic center to Relax, and I
> > > have
> > > submit it online.
> > >
> > > I remembered you said Relax Gui can not perfom model free analysis with
> > > only
> > > single field strength nmr data, how about the  Relax script mode ? I have
> > > just read the Relax user messages, the similar questions about single
> > > field
> > > strength data have been asked before.
> > >
> > > Thank you very much.
> > >
> > > With best regards,
> > >
> > > Mengjun Xue
> > >
> > >
> > >
> > >
> > >
> > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > >
> > > > 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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