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Originally posted by tmc@Dec 28 2005, 04:38 PM
Hello,
* I have some questions regarding the alignment matrix and I will be very much grateful if you could clarify my doubts.

Question 1:
1) I like to calculate the angle between the magnetic field and X,Y & Z axes of the alignment frame. For that, I have run PALES and got the values for Sxx, Sxy, Sxz, Syy & Syz. From Sxx value I have calculated cos(tx) and cos(ty) from Syy. Substituting these values in 1/2(3cos(tx)*cos(ty)), I calculated Sxy. But, this calculated value does not match with Sxy obtained from PALES.

When you run PALES, it should report you the magnitude of alignment, that is Sxx, Syy, Szz, etc. It should tell you the Euler angles correspondingly, right? So you can calculate the angles from these euler angles. For instance, angle between magnetic field and Szz is the Euler angle beta.

Question 2:
I found that the saupe parameters are in the order of 10 to the power -3 & above. However, an artile about the implimentation of svd procedure (Losonczi etal., J. Magnetic Resonance, 138,334-342 (1999)) indicates that the value of S's should lie between ~-1.0 to +1.0.

Hey, that is because they use different unit. It is scaled by a constant, Gamma(I)*Gamma(S)/r^3.

Question 3:
I found in the literature that Dconst= -mu*gamma(i)*gamma(j)*h/8*pi*pi*pi*r*r*r (Zweckstetter & Ad Bax, JACS, 2000, Tsui etal, 2000, J. Bio. Mol. NMR). However, an additional 2/3 term is found in the article by Bastiaan et al., Annual reports on NMR spectroscopy, 1987.
That is because they use different definition of S and R. Some guys use S and eta.

I will be very much thanful if you could help me to understand these.

Thank you
then

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