Hi Edward.
So, if I look in the Spin Viewer at residue 61 L after a TSMFK01, I
see the following values:
print cdp.mol[0].res
----------
Index Number Name
....
56 61 L
---------
print cdp.mol[0].res[56].spin[0].kA
2.65501706284
print cdp.mol[0].res[56].spin[0].dw
8.65652766346
print cdp.mol[0].res[56].spin[0].r2a
[8.9475124375463881]
I have to compare to article values reported as:
DOI: 10.1073/pnas.0509100103
Figure 2.
----------------------
Representative 15N CPMG relaxation dispersion curve measured on the
cross peaks from residue L61 in
folded ACBP at pH 5.3, 1 M GuHCl, and 40°C.
The dotted line represents a residue-specific fit of all parameters in Eq. 1:
ka = 11.3 +/- 0.7 s^{-1}
dw = (2.45 +/- 0.09) * 10^3 s^{-1}
R2 = 8.0 +/- 0.5 s^{-1}.
The solid line represents a global fit of ka to all protein residues
and a residue-specific
fit of "dw" and R2:
ka = 10.55 +/- 0.08 s^{-1}
dw = (2.44 +/- 0.08) * 10^3 s^{-1}
R2 = 8.4 +/- 0.3 s^{-1}.
--------------------------------
My dataset is for 0.48 M GuHCl, but anyway.
That means:
For kA:
2.655 rad.s * 2 * 3.14 = 16.6734 Hz.
Not totally close, but at least within discussion possibility.
Converting dw from ppm to Hz
print cdp.mol[0].res[56].spin[0].dw * cdp.spectrometer_frq['Z_A2'] * 1E-6
5192.97184369
Looks okay, but is this correct way of transforming the stored value?
R2, looks the same, but there is something wrong with a 2*pi factor.
Do you think this values looks reasonable or have I made a mistake somewhere?
Best
Troels
---------- Forwarded message ----------
From: <edward@xxxxxxxxxxxxx>
Date: 2013/9/4
Subject: r20799 - /branches/relax_disp/docs/latex/dispersion.tex
To: relax-commits@xxxxxxx
Author: bugman
Date: Wed Sep 4 15:13:47 2013
New Revision: 20799
URL: http://svn.gna.org/viewcvs/relax?rev=20799&view=rev
Log:
Fixes for the units in the dispersion parameter table in the user manual.
The units for dw are rad.s^-1 when used in the equations, but it is
stored internally as ppm.
Modified:
branches/relax_disp/docs/latex/dispersion.tex
Modified: branches/relax_disp/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion.tex?rev=20799&r1=20798&r2=20799&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion.tex (original)
+++ branches/relax_disp/docs/latex/dispersion.tex Wed Sep 4 15:13:47 2013
@@ -159,10 +159,10 @@
$\tex$ & $1 / (2 \kex)$ & Time of
exchange
& s.rad$^{-1}$ \\
$\pA$ & - & Population of
state A & - \\
$\pB$ & - & Population of
state B & - \\
-$\dw$ & - & Chemical shift
difference between the two states & ppm
(or rad.s$^{-1}$) \\
-$\Phiex$ & $\pA\pB\dw^2$ & Fast exchange
factor &
rad$^2$.s$^{-2}$ \\
-$\PhiexB$ & See \ref{eq: disp phiexB} on page \pageref{eq:
disp phiexB} & Fast exchange factor between sites A and B &
rad$^2$.s$^{-2}$ \\
-$\PhiexC$ & See \ref{eq: disp phiexC} on page \pageref{eq:
disp phiexC} & Fast exchange factor between sites A and C &
rad$^2$.s$^{-2}$ \\
+$\dw$ & - & Chemical shift
difference between the two states &
rad.s$^{-1}$ (stored as ppm) \\
+$\Phiex$ & $\pA\pB\dw^2$ & Fast exchange
factor &
rad$^2$.s$^{-2}$ (stored as ppm$^2$) \\
+$\PhiexB$ & See \ref{eq: disp phiexB} on page \pageref{eq:
disp phiexB} & Fast exchange factor between sites A and B &
rad$^2$.s$^{-2}$ (stored as ppm$^2$) \\
+$\PhiexC$ & See \ref{eq: disp phiexC} on page \pageref{eq:
disp phiexC} & Fast exchange factor between sites A and C &
rad$^2$.s$^{-2}$ (stored as ppm$^2$) \\
\bottomrule
\label{table: dispersion parameters}
\end{longtable}
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Fwd: r20799 - /branches/relax_disp/docs/latex/dispersion.tex