Author: bugman
Date: Sun Nov 17 17:39:33 2013
New Revision: 21488
URL: http://svn.gna.org/viewcvs/relax?rev=21488&view=rev
Log:
Added the 'TAP03' model to the relax user manual.
This is the Trott, Abergel and Palmer 2003 R1rho analytic model for 2-site
off-resonance exchange.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.
The 'TAP03' model was already partly in the manual, however it was listed as
unimplemented. All of
the tables and the dispersion chapter text has been updated for the model.
Modified:
branches/relax_disp/docs/latex/dispersion.tex
branches/relax_disp/docs/latex/dispersion_models.tex
branches/relax_disp/docs/latex/dispersion_software.tex
Modified: branches/relax_disp/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion.tex?rev=21488&r1=21487&r2=21488&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion.tex (original)
+++ branches/relax_disp/docs/latex/dispersion.tex Sun Nov 17 17:39:33 2013
@@ -104,6 +104,7 @@
\item[`DPL94':]\index{relaxation dispersion!DPL94 model} The
\citet{Davis94} 2-site fast exchange equation for off-resonance data with
parameters $\{\Ronerhoprime, \dots, \Phiex, \kex\}$. See Section~\ref{sect:
dispersion: DPL94 model} on page~\pageref{sect: dispersion: DPL94 model}.
\item[`M61 skew':]\index{relaxation dispersion!M61 skew model} The
\citet{Meiboom61} 2-site equation for all time scales with $\pA \gg \pB$ and
with parameters $\{\Ronerhoprime, \dots, \pA, \dw, \kex\}$. This model is
disabled by default in the dispersion auto-analysis. See Section~\ref{sect:
dispersion: M61 skew model} on page~\pageref{sect: dispersion: M61 skew
model}.
\item[`TP02':]\index{relaxation dispersion!TP02 model} The
\citet{TrottPalmer02} 2-site equation for all time scales with $\pA \gg \pB$
and with parameters $\{\Ronerhoprime, \dots, \pA, \dw, \kex\}$. See
Section~\ref{sect: dispersion: TP02 model} on page~\pageref{sect: dispersion:
TP02 model}.
+\item[`TAP03':]\index{relaxation dispersion!TAP03 model} The
\citet{Trott03} off-resonance 2-site analytic equation for all time scales
with the weak condition $\pA \gg \pB$ and with parameters $\{\Ronerhoprime,
\dots, \pA, \dw, \kex\}$.
\item[`MP05':]\index{relaxation dispersion!MP05 model} The
\citet{MiloushevPalmer05} off-resonance 2-site equation for all time scales
with parameters $\{\Ronerhoprime, \dots, \pA, \dw, \kex\}$. See
Section~\ref{sect: dispersion: MP05 model} on page~\pageref{sect: dispersion:
MP05 model}.
\end{description}
@@ -644,6 +645,44 @@
\end{itemize}
+% TAP03 model.
+%~~~~~~~~~~~~
+
+\subsection{The TAP03 2-site exchange $\Ronerho$ model}
+\label{sect: dispersion: TAP03 model}
+\index{relaxation dispersion!TAP03 model|textbf}
+
+This is the model for 2-site exchange for off-resonance $\Ronerho$-type
experiments from \citet{Trott03}.
+It is selected by setting the model to `TAP03'.
+The equation for the exchange process is
+\begin{align}
+ \Ronerho = & \Rone\cos^2\theta + \Ronerhoprime\sin^2\theta \nonumber \\
+ & + \left( \frac{1}{\gamma} \right)
+
\frac{\sin^2\hat\theta\pA\pB\dw^2\kex}{\hat\omega_\textrm{Aeff}^2\hat\omega_\textrm{Beff}^2/\hat\omega_\textrm{eff}^2
+ \kex^2 - 2\sin^2\hat\theta\pA\pB\dw^2 + (1 - \gamma)\omegaone^2},
+\end{align}
+
+in which
+\begin{subequations}
+\begin{align}
+ \delta_A &= \omegaA - \omegarf, \\
+ \delta_B &= \omegaB - \omegarf, \\
+ \sigma &= \pB\delta_A + \pA\delta_B, \\
+ \gamma &= 1 - \pA\pB\dw^2 \frac{\sigma^2 - \kex^2 + \omegaone^2}{\left(
\sigma^2 + \kex^2 + \omegaone^2 \right)^2}, \\
+ \hat\omega_\textrm{Aeff}^2 &= \gamma\omegaone^2 + \delta_A^2, \\
+ \hat\omega_\textrm{Beff}^2 &= \gamma\omegaone^2 + \delta_B^2, \\
+ \hat\omega_\textrm{eff}^2 &= \gamma\omegaone^2 + \aveoffset^2, \\
+ \hat\theta &= \arctan \left( \frac{\sqrt{\gamma}\omegaone}{\aveoffset}
\right).
+\end{align}
+\end{subequations}
+
+The equation is accurate when populations are less skewed than the `TP02'
model ($\pA \gg \pB$).
+Note that this model, as with the `TP02' model, has been superseded by the
`MP05' model in the next section.
+The reference for this equation is:
+\begin{itemize}
+\item \bibentry{Trott03}
+\end{itemize}
+
+
% MP05 model.
%~~~~~~~~~~~~
@@ -868,7 +907,6 @@
Some of the missing models include:
\begin{description}
-\item[`TAP03':]\index{relaxation dispersion!TAP03 model} The
$\Ronerho$-type data \citet{Trott03} 2-site analytic equation for all time
scales with parameters $\{\Ronerhoprime, \dots, \pA, \dw, \kex\}$.
\item[`TP04':]\index{relaxation dispersion!TP04 model} The $\Ronerho$-type
data \citet{TrottPalmer04} N-site analytic equation for all time scales with
parameters $\{\Ronerhoprime, \dots, \pone, \dots, \pN, \aveomega, \konetwo,
\dots\, \koneN\}$.
\item[`MMQ 3-site linear':]\index{relaxation dispersion!MMQ 3-site linear
model} The model of the numeric solution for linear 3-site exchange for
combined proton-heteronuclear SQ, ZQ, DQ and MQ (MMQ) CPMG-type data.
\item[`MMQ 3-site branched':]\index{relaxation dispersion!MMQ 3-site
branched model} Similar to the `MMQ 3-site linear' model but with one of the
$\kex$ parameters not set to zero.
Modified: branches/relax_disp/docs/latex/dispersion_models.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion_models.tex?rev=21488&r1=21487&r2=21488&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion_models.tex (original)
+++ branches/relax_disp/docs/latex/dispersion_models.tex Sun Nov 17 17:39:33
2013
@@ -77,7 +77,7 @@
DPL94 & Analytic & 2 & $\{\Ronerhoprime, \dots,
\Phiex, \kex\}$ & Fast exchange &
\citet{Davis94} \\
M61 skew & Analytic & 2 & $\{\Ronerhoprime, \dots, \pA,
\dw, \kex\}$ & $\pA \gg \pB$, on-resonance & \citet{Meiboom61}
\\
TP02 & Analytic & 2 & $\{\Ronerhoprime, \dots, \pA,
\dw, \kex\}$ & $\pA \gg \pB$, not fast exchange &
\citet{TrottPalmer02} \\
-TAP03\footnotemark[1] & Analytic & 2 & $\{\Ronerhoprime, \dots, \pA,
\dw, \kex\}$ & $\pA > \pB$ & \citet{Trott03} \\
+TAP03 & Analytic & 2 & $\{\Ronerhoprime, \dots, \pA,
\dw, \kex\}$ & Weak condition of $\pA \gg \pB$ & \citet{Trott03} \\
TP04\footnotemark[1] & Analytic & N & $\{\Ronerhoprime, \dots,
\pone, \dots, \pN, \aveomega, \konetwo, \dots\, \koneN\}$ & One site
dominant & \citet{TrottPalmer04} \\
MP05 & Analytic & 2 & $\{\Ronerhoprime, \dots, \pA,
\dw, \kex\}$ & $\pA > \pB$ &
\citet{MiloushevPalmer05} \\
NS R1rho 2-site & Numeric & 2 & $\{\Ronerhoprime, \dots, \pA,
\dw, \kex\}$ & $\pA > \pB$ & - \\
Modified: branches/relax_disp/docs/latex/dispersion_software.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion_software.tex?rev=21488&r1=21487&r2=21488&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion_software.tex (original)
+++ branches/relax_disp/docs/latex/dispersion_software.tex Sun Nov 17
17:39:33 2013
@@ -66,7 +66,7 @@
M61 & \no & \no & \no & \no & \no & \no & \no
& \no & \yes \\
DPL94 & \no & \no & \no & \no & \no & \no & \no
& \no & \yes \\
TP02 & \no & \yes & \no & \no & \no & \no & \no
& \no & \yes \\
-TAP03 & \no & \no & \no & \no & \no & \no & \no
& \no & \no \\
+TAP03 & \no & \no & \no & \no & \no & \no & \no
& \no & \yes \\
TP04 & \no & \no & \no & \no & \no & \no & \no
& \no & \no \\
MP05 & \no & \no & \no & \no & \no & \no & \no
& \no & \yes \\
NS 2-site & \no & \yes & \no & \no & \no & \no & ?
& \no & \yes \\
r21488 - in /branches/relax_disp/docs/latex: dispersion.tex dispersion_models.tex dispersion_software.tex