Hi,
Yes, this does seem like a difference between the steady-state NOE
(NOE) verses the cross-relaxation rate (sigma NOE). Actually all I
did was simply copy Equation 5 of Zhang, P., Dayie, K. T., and Wagner,
G. (1997) JMB, 272, 443-455 rather than calculate it from the C
matricies of the original reduced spectral density mapping paper of
Lefevre, J., Dayie, K., Peng, J., and Wagner, G. (1996) Biochem., 35,
2674-2686.
Edward
On 7/3/06, Chris MacRaild <c.a.macraild@xxxxxxxxxxx> wrote:
Hi Ruth,
I'm fairly sure this is just a difference in definitions of sigma_noe.
relax defines sigma_noe (the cross-relaxation rate) as:
(noe - 1.0) * r1 * self.data.gx / self.data.gh
see maths_fns/jw_mapping.py at about line 67. self.data.gx and
self.data.gh are the respective gyromagnetic ratios. So R1 is accounted
for appropriately.
This is the convention used eg. in Atkinson and Kieffer's review (Prog.
NMR Spec. 44, 141-187 (2004)), and the equations for J(0), J(wH) and
J(wN) (lines 92-98 in maths_fns/jw_mapping.py) are exactly equivalent to
their eq. 6
Chris
On Mon, 2006-07-03 at 13:40 +0100, Ruth Boetzel wrote:
> Hi there!
>
> I'm trying to use the spectral density mapping module and have a problem
> with the equation for J(0).
> In the program J(0) is given as
> j0 = -1.5 / (3.0*d + c) * (0.5*r1 - r2 + 0.6*sigma_noe)
>
> However, when I work out the equation from the literature (e.g. Farrow et
> al., J. Biomol. NMR, 6, 1530162, 1995, equations 5,6,7) I get
> j0 = -1.5 / (3.0*d + c) * (0.5*r1 - r2 + 0.6*sigma_noe*r1)
> I can't see how it is possible to get rid of r1 in the sigma_noe term. A
> colleague of mine also tried and got the same result as I did.
> Am I missing something or is the r1 term missing?
>
> Cheers
> Ruth
>
>
> ********************************************
> * Dr Ruth Boetzel *
> * School of Chemical Sciences and Pharmacy *
> * University of East Anglia *
> * Norwich NR4 7TJ *
> * UK *
> * Phone: +44-1603-592001 *
> * E-Mail: r.boetzel@xxxxxxxxx *
> ********************************************
>
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Re: Reduced spectral density mapping