Author: bugman
Date: Wed Nov 6 15:30:19 2013
New Revision: 21396
URL: http://svn.gna.org/viewcvs/relax?rev=21396&view=rev
Log:
Expanded the numeric dispersion models to include the linear and branched
3-site models in the manual.
Modified:
branches/relax_disp/docs/latex/dispersion.tex
branches/relax_disp/docs/latex/dispersion_models.tex
branches/relax_disp/docs/latex/dispersion_params.tex
branches/relax_disp/docs/latex/relax.tex
Modified: branches/relax_disp/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion.tex?rev=21396&r1=21395&r2=21396&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion.tex (original)
+++ branches/relax_disp/docs/latex/dispersion.tex Wed Nov 6 15:30:19 2013
@@ -276,16 +276,16 @@
In this situation, the following relationships hold
\begin{subequations}
\begin{align}
- &\kB \approx \kexB = \kAB + \kBA , \\
- &\kC \approx \kexC = \kAC + \kCA ,
+ &\kB \approx \kexAB = \kAB + \kBA , \\
+ &\kC \approx \kexAC = \kAC + \kCA ,
\end{align}
\end{subequations}
and
\begin{subequations}
\begin{align}
- &\PhiexB = \overline{\Phiex} \frac{\kexB^2 \left( \overline{\kex} -
\kexC \right)}{\kex^2 \left( \kex - \kexC \right)} , \label{eq: disp phiexB}
\\
- &\PhiexC = \overline{\Phiex} \frac{\kexC^2 \left( \overline{\kex} -
\kexB \right)}{\kex^2 \left( \kexC - \kexB \right)} , \label{eq: disp phiexC}
+ &\PhiexB = \overline{\Phiex} \frac{(\kexAB)^2 \left( \overline{\kex} -
\kexAC \right)}{\kex^2 \left( \kex - \kexAC \right)} , \label{eq: disp
phiexB} \\
+ &\PhiexC = \overline{\Phiex} \frac{(\kexAC)^2 \left( \overline{\kex} -
\kexAB \right)}{\kex^2 \left( \kexAC - \kexAB \right)} , \label{eq: disp
phiexC}
\end{align}
\end{subequations}
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=21396&r1=21395&r2=21396&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion_models.tex (original)
+++ branches/relax_disp/docs/latex/dispersion_models.tex Wed Nov 6 15:30:19
2013
@@ -1,20 +1,26 @@
-\begin{sidewaystable}
+\begin{landscape}
\begin{center}
\begin{small}
+
+% The longtable environment.
+\begin{longtable}{llllll}
% Caption.
\caption[The dispersion models.]{The dispersion models supported by relax.}
-% The tabular environment.
-\begin{tabular}{lllcll}
+% Header.
+\\
+\toprule
+Model name & Solution & Sites & Parameters
& Restrictions & Reference \\
+\midrule
+\endhead
-\\[-5pt]
-\toprule
+% Footer.
+\bottomrule
+\endfoot
-% Headings.
-Model code & Solution & Sites & Parameters
& Restriction & Reference \\
-
-\midrule
+% Label.
+\label{table: dispersion models}
\\[-5pt]
% Experiment independent models.
@@ -31,7 +37,8 @@
\cline{1-1}
\\[-5pt]
LM63 & Analytic & 2 & $\{\Rtwozero, \dots, \Phiex,
\kex\}$ & Fast exchange &
\citet{LuzMeiboom63} \\
-LM63 3-site & Analytic & 3 & $\{\Rtwozero, \dots, \PhiexB,
\kB, \PhiexC, \kC\}$ & Fast exchange, $\pA > \pB$ and $\pA > \pC$ &
\citet{LuzMeiboom63} \\
+LM63 3-site & Analytic & 3 & $\{\Rtwozero, \dots, \PhiexB,
\kB, \PhiexC, \kC\}$ & Fast exchange, $\pA > \pB$ and &
\citet{LuzMeiboom63} \\
+ & & &
& $\pA > \pC$ \\
CR72 & Analytic & 2 & $\{\Rtwozero, \dots, \pA, \dw,
\kex\}$ & $\pA > \pB$ &
\citet{CarverRichards72} \\
CR72 full & Analytic & 2 & $\{\RtwozeroA, \RtwozeroB,
\dots, \pA, \dw, \kex\}$ & $\pA > \pB$ &
\citet{CarverRichards72} \\
IT99 & Analytic & 2 & $\{\Rtwozero, \dots, \pA, \dw,
\kex\}$ & $\pA \gg \pB$ &
\citet{IshimaTorchia99} \\
@@ -43,38 +50,42 @@
NS CPMG 2-site star full & Numeric & 2 & $\{\RtwozeroA, \RtwozeroB,
\dots, \pA, \dw, \kex\}$ & $\pA > \pB$ & - \\
\\[-5pt]
-% R1rho-type models.
-$\Ronerho$-type \\
-\cline{1-1}
-\\[-5pt]
-M61 & Analytic & 2 & $\{\Ronerhoprime, \dots, \Phiex,
\kex\}$ & Fast exchange, on-resonance, $\Rone = \Rtwo$ &
\citet{Meiboom61} \\
-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 & $\{\Ronerhoprime, \dots, \pA, \dw,
\kex\}$ & Not fast exchange & \citet{TrottPalmer02} \\
-TP04 & 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 & $\{\Ronerhoprime, \dots, \pA, \dw,
\kex\}$ & $\pA > \pB$ & - \\
-
-\\[-5pt]
% MQ CPMG-type models.
MQ CPMG-type \\
\cline{1-1}
\\[-5pt]
-MQ CR72 & Analytic & 2 & $\{\Rtwozero, \dots, \pA, \dw, \dwH,
\kex\}$ & $\pA > \pB$ & \citet{Korzhnev04a} \\
+MQ CR72 & Analytic & 2 & $\{\Rtwozero, \dots, \pA, \dw,
\dwH, \kex\}$ & $\pA > \pB$ &
\citet{Korzhnev04a} \\
\\[-5pt]
% SQ, ZQ, DQ and MQ CPMG-type models.
-SQ, ZQ, DQ and MQ CPMG-type \\
+MMQ CPMG-type \\
\cline{1-1}
\\[-5pt]
-MMQ 2-site & Numeric & 2 & $\{\Rtwozero, \dots, \pA, \dw, \dwH,
\kex\}$ & $\pA > \pB$ & \citet{Korzhnev05} \\
+MMQ 2-site & Numeric & 2 & $\{\Rtwozero, \dots, \pA, \dw,
\dwH, \kex\}$ & $\pA > \pB$ & \citet{Korzhnev05}
\\
+MMQ 3-site (linear) & Numeric & 3 & $\{\Rtwozero, \dots, \pA, \pB,
\dwAB, \dwAC,$ & $\pA > \pB$ and $\pA > \pC$ & \citet{Korzhnev05}
\\
+ & & & $\dwHAB, \dwHAC, \kexAB,
\kexAC\}$ \\
+MMQ 3-site (branched) & Numeric & 3 & $\{\Rtwozero, \dots, \pA, \pB,
\dwAB, \dwAC$ & $\pA > \pB$ and $\pA > \pC$ & \citet{Korzhnev05}
\\
+ & & & $, \dwHAB, \dwHAC, \dwHBC,
\kexAB, \kexAC, \kexBC\}$ \\
-\bottomrule
+% R1rho-type models.
+\clearpage
+$\Ronerho$-type \\
+\cline{1-1}
+\\[-5pt]
+M61 & Analytic & 2 & $\{\Ronerhoprime, \dots,
\Phiex, \kex\}$ & Fast exchange, on-resonance, &
\citet{Meiboom61} \\
+ & & &
& $\Rone = \Rtwo$ \\
+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 & $\{\Ronerhoprime, \dots, \pA,
\dw, \kex\}$ & Not fast exchange &
\citet{TrottPalmer02} \\
+TP04 & Analytic & N & $\{\Ronerhoprime, \dots,
\pone, \dots, \pN, \aveom ega, \konetwo, \dots\, \koneN\}$ & One site
dominant & \citet{TrottPalmer04} \\
+MP05 & Analytic & 2 & $\{\Ronerhoprime, \dots, \pA,
\dw, \kex\}$ & $\pA > \pB$ &
\citet{MiloushevPalmer05} \\
+NS R1rho 2-site & Numeric & 2 & $\{\Ronerhoprime, \dots, \pA,
\dw, \kex\}$ & $\pA > \pB$ & - \\
+NS R1rho 3-site (linear) & Numeric & 3 & $\{\Ronerhoprime, \dots, \pA,
\pB, \dwAB, \dwAC,$ & $\pA > \pB$ and $\pA > \pC$ & - \\
+ & & & $\dwHAB, \dwHAC, \kexAB,
\kexAC\}$ \\
+NS R1rho 3-site (branched) & Numeric & 3 & $\{\Ronerhoprime, \dots, \pA,
\pB, \dwAB, \dwAC$ & $\pA > \pB$ and $\pA > \pC$ & - \\
+ & & & $, \dwHAB, \dwHAC, \dwHBC,
\kexAB, \kexAC, \kexBC\}$ \\
-% Label.
-\label{table: dispersion models}
-
-\end{tabular}
+\end{longtable}
\end{small}
\end{center}
-\end{sidewaystable}
+\end{landscape}
Modified: branches/relax_disp/docs/latex/dispersion_params.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion_params.tex?rev=21396&r1=21395&r2=21396&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion_params.tex (original)
+++ branches/relax_disp/docs/latex/dispersion_params.tex Wed Nov 6 15:30:19
2013
@@ -1,20 +1,26 @@
-\begin{sidewaystable}
+\begin{landscape}
\begin{center}
\begin{small}
+
+% The tabular environment.
+\begin{longtable}{llll}
% Caption.
\caption[The parameters of relaxation dispersion.]{The parameters of
relaxation dispersion.}
-% The tabular environment.
-\begin{tabular}{llll}
+% Header.
+\\
+\toprule
+Parameter & Equation & Description
& Units \\
+\midrule
+\endhead
-\\[-5pt]
-\toprule
+% Footer.
+\bottomrule
+\endfoot
-% Headings.
-Parameter & Equation & Description
& Units \\
-
-\midrule
+% Label.
+\label{table: dispersion parameters}
$\nucpmg$ & $1 / (2 \taucpmg)$ & CPMG frequency
& Hz \\
$\taucpmg$ & $1 / (2 \nucpmg)$ & Delay between CPMG
$\pi$ pulses & s \\
@@ -36,25 +42,27 @@
$\kAB$ & $\pB\kex$ & The forward exchange
rate from state A to state B & rad.s$^{-1}$ \\
$\kBA$ & $\pA\kex$ & The reverse exchange
rate from state B to state A & rad.s$^{-1}$ \\
$\kex$ & $1 / \tex$ & Chemical exchange rate
constant & rad.s$^{-1}$ \\
-$\kexB$ & $\kAB + \kBA$ & Chemical exchange rate
constant between sites A and B & rad.s$^{-1}$ \\
-$\kexC$ & $\kAC + \kCA$ & Chemical exchange rate
constant between sites A and C & rad.s$^{-1}$ \\
-$\kB$ & $\approx \kexB$ & Approximate chemical
exchange rate constant between sites A and B & rad.s$^{-1}$ \\
-$\kC$ & $\approx \kexC$ & Approximate chemical
exchange rate constant between sites A and C & rad.s$^{-1}$ \\
+$\kexAB$ & $\kAB + \kBA$ & Chemical exchange rate
constant between sites A and B & rad.s$^{-1}$ \\
+$\kexAC$ & $\kAC + \kCA$ & Chemical exchange rate
constant between sites A and C & rad.s$^{-1}$ \\
+$\kexBC$ & $\kBC + \kCB$ & Chemical exchange rate
constant between sites B and C & rad.s$^{-1}$ \\
+$\kB$ & $\approx \kexAB$ & Approximate chemical
exchange rate constant between sites A and B & rad.s$^{-1}$ \\
+$\kC$ & $\approx \kexAC$ & Approximate chemical
exchange rate constant between sites A and C & rad.s$^{-1}$ \\
$\tex$ & $1 / \kex$ & Time of exchange
& s.rad$^{-1}$ \\
$\pA$ & - & Population of state A
& - \\
$\pB$ & - & Population of state B
& - \\
-$\dw$ & - & Chemical shift
difference between the two states & rad.s$^{-1}$
(stored as ppm) \\
+$\dw$ & - & Chemical shift
difference between the two states (A and B) & rad.s$^{-1}$
(stored as ppm) \\
+$\dwAB$ & - & Chemical shift
difference between sites A and B & rad.s$^{-1}$
(stored as ppm) \\
+$\dwAC$ & - & Chemical shift
difference between sites A and C & rad.s$^{-1}$
(stored as ppm) \\
+$\dwBC$ & - & Chemical shift
difference between sites B and C & rad.s$^{-1}$
(stored as ppm) \\
$\dwH$ & - & Proton chemical shift
difference between the two states (for MQ data) & rad.s$^{-1}$
(stored as ppm) \\
+$\dwHAB$ & - & Proton chemical shift
difference between sites A and B (for MQ data) & rad.s$^{-1}$
(stored as ppm) \\
+$\dwHAC$ & - & Proton chemical shift
difference between sites A and C (for MQ data) & rad.s$^{-1}$
(stored as ppm) \\
+$\dwHBC$ & - & Proton chemical shift
difference between sites B and C (for MQ data) & 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.
-\label{table: dispersion parameters}
-
-\end{tabular}
+\end{longtable}
\end{small}
\end{center}
-\end{sidewaystable}
+\end{landscape}
Modified: branches/relax_disp/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/relax.tex?rev=21396&r1=21395&r2=21396&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/relax.tex (original)
+++ branches/relax_disp/docs/latex/relax.tex Wed Nov 6 15:30:19 2013
@@ -14,6 +14,7 @@
\usepackage{longtable}
\usepackage{tabularx}
\usepackage{rotating}
+\usepackage{lscape}
% Nth.
\usepackage[super]{nth}
@@ -136,13 +137,18 @@
\newcommand{\dw}{\Delta\omega}
\newcommand{\dwAB}{\Delta\omega_\textrm{AB}}
\newcommand{\dwAC}{\Delta\omega_\textrm{AC}}
-\newcommand{\dwH}{\Delta\omega_{\scriptscriptstyle\mathrm{H}}}
+\newcommand{\dwBC}{\Delta\omega_\textrm{BC}}
+\newcommand{\dwH}{\Delta\omega^{\scriptscriptstyle\mathrm{H}}}
+\newcommand{\dwHAB}{\Delta\omega^{\scriptscriptstyle\mathrm{H}}_\textrm{AB}}
+\newcommand{\dwHAC}{\Delta\omega^{\scriptscriptstyle\mathrm{H}}_\textrm{AC}}
+\newcommand{\dwHBC}{\Delta\omega^{\scriptscriptstyle\mathrm{H}}_\textrm{BC}}
\newcommand{\konetwo}{\textrm{k}_\textrm{12}}
\newcommand{\konethree}{\textrm{k}_\textrm{13}}
\newcommand{\koneN}{\textrm{k}_\textrm{1N}}
\newcommand{\kex}{\textrm{k}_\textrm{ex}}
-\newcommand{\kexB}{\textrm{k}_\textrm{ex,B}}
-\newcommand{\kexC}{\textrm{k}_\textrm{ex,C}}
+\newcommand{\kexAB}{\textrm{k}_\textrm{ex}^\textrm{AB}}
+\newcommand{\kexAC}{\textrm{k}_\textrm{ex}^\textrm{AC}}
+\newcommand{\kexBC}{\textrm{k}_\textrm{ex}^\textrm{BC}}
\newcommand{\kA}{\textrm{k}_\textrm{A}}
\newcommand{\kB}{\textrm{k}_\textrm{B}}
\newcommand{\kC}{\textrm{k}_\textrm{C}}
r21396 - in /branches/relax_disp/docs/latex: dispersion.tex dispersion_models.tex dispersion_params.tex relax.tex