Author: bugman Date: Mon Oct 12 11:39:20 2015 New Revision: 28026 URL: http://svn.gna.org/viewcvs/relax?rev=28026&view=rev Log: Removed the newparagraph and newsubparagraph definitions from the LaTeX manual. These were causing conflicts with latex2html, preventing the HTML version of the manual at http://www.nmr-relax.com/manual/index.html from being compiled. These definitions are unnecessary for the current set up of the sectioning in the manual. Modified: trunk/docs/latex/frame_order/models.tex trunk/docs/latex/frame_order/pcs_numerical_integration.tex trunk/docs/latex/relax.tex Modified: trunk/docs/latex/frame_order/models.tex URL: http://svn.gna.org/viewcvs/relax/trunk/docs/latex/frame_order/models.tex?rev=28026&r1=28025&r2=28026&view=diff ============================================================================== --- trunk/docs/latex/frame_order/models.tex (original) +++ trunk/docs/latex/frame_order/models.tex Mon Oct 12 11:39:20 2015 @@ -88,7 +88,7 @@ where surface normalisation factor is 1. -\newparagraph{Rigid \nth{1} degree frame order} +\paragraph{Rigid \nth{1} degree frame order} The \nth{1} degree frame order matrix with tensor rank-2 is the identity matrix \begin{subequations} \label{eq: rigid 1st degree frame order matrix} @@ -103,7 +103,7 @@ \end{subequations} -\newparagraph{Rigid \nth{2} degree frame order} +\paragraph{Rigid \nth{2} degree frame order} The \nth{2} degree frame order matrix with tensor rank-4 is the identity matrix \begin{subequations} \label{eq: rigid 2nd degree frame order matrix} @@ -254,7 +254,7 @@ \end{subequations} -\newparagraph{Rotor \nth{1} degree frame order} +\paragraph{Rotor \nth{1} degree frame order} The \nth{1} degree frame order matrix with tensor rank-2 is \begin{subequations} \label{eq: rotor 1st degree frame order matrix} @@ -270,7 +270,7 @@ \end{subequations} -\newparagraph{Rotor \nth{2} degree frame order} +\paragraph{Rotor \nth{2} degree frame order} The \nth{2} degree frame order matrix with tensor rank-4 is \begin{subequations} @@ -320,7 +320,7 @@ \end{subequations} -\newsubparagraph[Frame order matrix simulation and calculation]{Rotor frame order matrix simulation and calculation} +\subparagraph[Frame order matrix simulation and calculation]{Rotor frame order matrix simulation and calculation} The frame order matrix element simulation script from Section~\ref{sect: frame order simulation}, page~\pageref{sect: frame order simulation} was used to compare the implementation of equations~\ref{eq: rotor 1st degree frame order matrix} and~\ref{eq: rotor 2nd degree frame order matrix} above. Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and calculated, both within and out of the motional eigenframe. @@ -413,7 +413,7 @@ \end{subequations} -\newparagraph{Free rotor \nth{1} degree frame order} +\paragraph{Free rotor \nth{1} degree frame order} The \nth{1} degree frame order matrix with tensor rank-2 is \begin{subequations} \label{eq: free rotor 1st degree frame order matrix} @@ -429,7 +429,7 @@ \end{subequations} -\newparagraph{Free rotor \nth{2} degree frame order} +\paragraph{Free rotor \nth{2} degree frame order} The frame order matrix in Kronecker product notation is fixed as \begin{equation} \label{eq: free rotor 2nd degree frame order matrix} @@ -448,7 +448,7 @@ \end{equation} -\newsubparagraph[Frame order matrix simulation and calculation]{Free rotor frame order matrix simulation and calculation} +\subparagraph[Frame order matrix simulation and calculation]{Free rotor frame order matrix simulation and calculation} The frame order matrix element simulation script from Section~\ref{sect: frame order simulation}, page~\pageref{sect: frame order simulation} was used to compare the implementation of equations~\ref{eq: free rotor 1st degree frame order matrix} and~\ref{eq: free rotor 2nd degree frame order matrix} above. Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and calculated, both within and out of the motional eigenframe. @@ -596,7 +596,7 @@ \end{subequations} -\newparagraph{Isotropic cone \nth{1} degree frame order} +\paragraph{Isotropic cone \nth{1} degree frame order} The \nth{1} degree frame order matrix with tensor rank-2 is \begin{subequations} \label{eq: iso cone 1st degree frame order matrix} @@ -612,7 +612,7 @@ \end{subequations} -\newparagraph{Isotropic cone \nth{2} degree frame order} +\paragraph{Isotropic cone \nth{2} degree frame order} The \nth{2} degree frame order matrix with tensor rank-4 consists of the following elements, using Kronecker product double indices from 0 to 8 \begin{subequations} \label{eq: iso cone 2nd degree frame order matrix} @@ -642,7 +642,7 @@ \end{subequations} -\newsubparagraph[Frame order matrix simulation and calculation]{Isotropic cone frame order matrix simulation and calculation} +\subparagraph[Frame order matrix simulation and calculation]{Isotropic cone frame order matrix simulation and calculation} The frame order matrix element simulation script from Section~\ref{sect: frame order simulation}, page~\pageref{sect: frame order simulation} was used to compare the implementation of equations~\ref{eq: iso cone 1st degree frame order matrix} and~\ref{eq: iso cone 2nd degree frame order matrix} above. Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and calculated, both within and out of the motional eigenframe. @@ -736,7 +736,7 @@ \end{subequations} -\newparagraph{Torsionless isotropic cone \nth{1} degree frame order} +\paragraph{Torsionless isotropic cone \nth{1} degree frame order} The \nth{1} degree frame order matrix with tensor rank-2 is \begin{subequations} \label{eq: iso cone, torsionless 1st degree frame order matrix} @@ -752,7 +752,7 @@ \end{subequations} -\newparagraph{Torsionless isotropic cone \nth{2} degree frame order} +\paragraph{Torsionless isotropic cone \nth{2} degree frame order} The \nth{2} degree frame order matrix with tensor rank-4 consists of the following elements, using Kronecker product double indices from 0 to 8 \begin{subequations} @@ -808,7 +808,7 @@ \end{align} \end{subequations} -\newsubparagraph[Frame order matrix simulation and calculation]{Torsionless isotropic cone frame order matrix simulation and calculation} +\subparagraph[Frame order matrix simulation and calculation]{Torsionless isotropic cone frame order matrix simulation and calculation} The frame order matrix element simulation script from Section~\ref{sect: frame order simulation}, page~\pageref{sect: frame order simulation} was used to compare the implementation of equations~\ref{eq: iso cone, torsionless 1st degree frame order matrix} and~\ref{eq: iso cone, torsionless 2nd degree frame order matrix} above. Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and calculated, both within and out of the motional eigenframe. @@ -902,7 +902,7 @@ \end{subequations} -\newparagraph{Free rotor isotropic cone \nth{1} degree frame order} +\paragraph{Free rotor isotropic cone \nth{1} degree frame order} The \nth{1} degree frame order matrix with tensor rank-2 is \begin{subequations} \label{eq: iso cone, free rotor 1st degree frame order matrix} @@ -918,7 +918,7 @@ \end{subequations} -\newparagraph{Free rotor isotropic cone \nth{2} degree frame order} +\paragraph{Free rotor isotropic cone \nth{2} degree frame order} The \nth{2} degree frame order matrix with tensor rank-4 consists of the following elements, using Kronecker product double indices from 0 to 8 @@ -949,7 +949,7 @@ \end{subequations} -\newsubparagraph[Frame order matrix simulation and calculation]{Free rotor isotropic cone frame order matrix simulation and calculation} +\subparagraph[Frame order matrix simulation and calculation]{Free rotor isotropic cone frame order matrix simulation and calculation} The frame order matrix element simulation script from Section~\ref{sect: frame order simulation}, page~\pageref{sect: frame order simulation} was used to compare the implementation of equations~\ref{eq: iso cone, free rotor 1st degree frame order matrix} and~\ref{eq: iso cone, free rotor 2nd degree frame order matrix} above. Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and calculated, both within and out of the motional eigenframe. @@ -1237,7 +1237,7 @@ \end{align} \end{subequations} -\newparagraph{Pseudo-ellipse \nth{1} degree frame order} +\paragraph{Pseudo-ellipse \nth{1} degree frame order} The \nth{1} degree frame order matrix with tensor rank-2 consists of the following elements \begin{subequations} \label{eq: pseudo-ellipse 1st degree frame order matrix} @@ -1264,7 +1264,7 @@ As the trigonometric functions of $\conethetamax$ cannot be integrated, these components must be numerically integrated. -\newparagraph{Pseudo-ellipse \nth{2} degree frame order} +\paragraph{Pseudo-ellipse \nth{2} degree frame order} The \nth{2} degree frame order matrix with tensor rank-4 consists of the following elements, using Kronecker product double indices from 0 to 8 \begin{subequations} \label{eq: pseudo-ellipse 2nd degree frame order matrix} @@ -1442,7 +1442,7 @@ All other frame order matrix elements can be numerically shown to be zero. -\newsubparagraph[Frame order matrix simulation and calculation]{Pseudo-ellipse frame order matrix simulation and calculation} +\subparagraph[Frame order matrix simulation and calculation]{Pseudo-ellipse frame order matrix simulation and calculation} The frame order matrix element simulation script from Section~\ref{sect: frame order simulation}, page~\pageref{sect: frame order simulation} was used to compare the implementation of equations~\ref{eq: pseudo-ellipse 1st degree frame order matrix} and~\ref{eq: pseudo-ellipse 2nd degree frame order matrix} above. Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and calculated, both within and out of the motional eigenframe. @@ -1588,7 +1588,7 @@ \end{subequations} -\newparagraph{Torsionless pseudo-ellipse \nth{1} degree frame order} +\paragraph{Torsionless pseudo-ellipse \nth{1} degree frame order} The \nth{1} degree frame order matrix with tensor rank-2 consists of the following elements \begin{subequations} \label{eq: pseudo-ellipse, torsionless 1st degree frame order matrix} @@ -1615,7 +1615,7 @@ As the trigonometric functions of $\conethetamax$ cannot be symbolically integrated, these components must be numerically integrated. -\newparagraph{Torsionless pseudo-ellipse \nth{2} degree frame order} +\paragraph{Torsionless pseudo-ellipse \nth{2} degree frame order} The \nth{2} degree frame order matrix with tensor rank-4 consists of the following elements, using Kronecker product double indices from 0 to 8 \begin{subequations} \label{eq: pseudo-ellipse, torsionless 2nd degree frame order matrix} @@ -1742,7 +1742,7 @@ \end{subequations} -\newsubparagraph[Frame order matrix simulation and calculation]{Torsionless pseudo-ellipse frame order matrix simulation and calculation} +\subparagraph[Frame order matrix simulation and calculation]{Torsionless pseudo-ellipse frame order matrix simulation and calculation} The frame order matrix element simulation script from Section~\ref{sect: frame order simulation}, page~\pageref{sect: frame order simulation} was used to compare the implementation of equations~\ref{eq: pseudo-ellipse, torsionless 1st degree frame order matrix} and~\ref{eq: pseudo-ellipse, torsionless 2nd degree frame order matrix} above. Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and calculated, both within and out of the motional eigenframe. @@ -1878,7 +1878,7 @@ \end{subequations} -\newparagraph{Free rotor pseudo-ellipse \nth{1} degree frame order} +\paragraph{Free rotor pseudo-ellipse \nth{1} degree frame order} The \nth{1} degree frame order matrix with tensor rank-2 is \begin{subequations} \label{eq: pseudo-ellipse, free rotor 1st degree frame order matrix} @@ -1897,7 +1897,7 @@ \end{subequations} -\newparagraph{Free rotor pseudo-ellipse \nth{2} degree frame order} +\paragraph{Free rotor pseudo-ellipse \nth{2} degree frame order} The \nth{2} degree frame order matrix with tensor rank-4 consists of the following elements, using Kronecker product double indices from 0 to 8 \begin{subequations} \label{eq: pseudo-ellipse, free rotor 2nd degree frame order matrix} @@ -2001,7 +2001,7 @@ \end{subequations} -\newsubparagraph[Frame order matrix simulation and calculation]{Free rotor pseudo-ellipse frame order matrix simulation and calculation} +\subparagraph[Frame order matrix simulation and calculation]{Free rotor pseudo-ellipse frame order matrix simulation and calculation} The frame order matrix element simulation script from Section~\ref{sect: frame order simulation}, page~\pageref{sect: frame order simulation} was used to compare the implementation of equations~\ref{eq: pseudo-ellipse, free rotor 1st degree frame order matrix} and~\ref{eq: pseudo-ellipse, free rotor 2nd degree frame order matrix} above. Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and calculated, both within and out of the motional eigenframe. @@ -2180,7 +2180,7 @@ \end{subequations} -\newparagraph{Double rotor \nth{1} degree frame order} +\paragraph{Double rotor \nth{1} degree frame order} The un-normalised \nth{1} degress frame order matrix with tensor rank-2 is \begin{subequations} @@ -2206,7 +2206,7 @@ \end{pmatrix}. \end{equation} -\newparagraph{Double rotor \nth{2} degree frame order} +\paragraph{Double rotor \nth{2} degree frame order} The \nth{2} degree frame order matrix with tensor rank-4 consists of the following elements, using Kronecker product double indices from 0 to 8 \begin{subequations} \label{eq: double rotor 2nd degree frame order matrix} @@ -2237,7 +2237,7 @@ -\newsubparagraph[Frame order matrix simulation and calculation]{Double rotor frame order matrix simulation and calculation} +\subparagraph[Frame order matrix simulation and calculation]{Double rotor frame order matrix simulation and calculation} The frame order matrix element simulation script from Section~\ref{sect: frame order simulation}, page~\pageref{sect: frame order simulation} was used to compare the implementation of equations~\ref{eq: double rotor 1st degree frame order matrix} and~\ref{eq: double rotor 2nd degree frame order matrix} above. Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and calculated, both within and out of the motional eigenframe. Modified: trunk/docs/latex/frame_order/pcs_numerical_integration.tex URL: http://svn.gna.org/viewcvs/relax/trunk/docs/latex/frame_order/pcs_numerical_integration.tex?rev=28026&r1=28025&r2=28026&view=diff ============================================================================== --- trunk/docs/latex/frame_order/pcs_numerical_integration.tex (original) +++ trunk/docs/latex/frame_order/pcs_numerical_integration.tex Mon Oct 12 11:39:20 2015 @@ -138,7 +138,7 @@ The modelling of the $\sigma$ torsion angle gives a number of categories of related models, those with no torsion, those with restricted torsion, and the free rotors. -\newparagraph{No torsion} +\paragraph{No torsion} When $\sigma = 0$, the following models are defined: \begin{itemize} @@ -148,7 +148,7 @@ \end{itemize} -\newparagraph{Restricted torsion} +\paragraph{Restricted torsion} When $0 < \sigma < \pi$, the following models are defined: \begin{itemize} @@ -158,7 +158,7 @@ \end{itemize} -\newparagraph{Free rotors} +\paragraph{Free rotors} When $\sigma = \pi$, i.e.\ there is no torsional restriction, the following models are defined: \begin{itemize} @@ -168,7 +168,7 @@ \end{itemize} -\newparagraph{Multiple torsion angles} +\paragraph{Multiple torsion angles} This covers a single model -- the double rotor. @@ -179,7 +179,7 @@ There are three major parameter categories -- the average domain position, the eigenframe of the motion, and the amplitude of the motion. -\newparagraph{Average domain position} +\paragraph{Average domain position} Let the translational parameters be \begin{equation} @@ -200,7 +200,7 @@ \end{subequations} -\newparagraph{The motional eigenframe} +\paragraph{The motional eigenframe} This consists of either the full eigenframe or a single axis, combined with the pivot point(s) defining the origin of the frame(s) within the PDB space. The eigenframe parameters themselves are @@ -221,7 +221,7 @@ \end{subequations} -\newparagraph{The rigid body ordering} +\paragraph{The rigid body ordering} The parameters of order are \begin{equation} Modified: trunk/docs/latex/relax.tex URL: http://svn.gna.org/viewcvs/relax/trunk/docs/latex/relax.tex?rev=28026&r1=28025&r2=28026&view=diff ============================================================================== --- trunk/docs/latex/relax.tex (original) +++ trunk/docs/latex/relax.tex Mon Oct 12 11:39:20 2015 @@ -28,18 +28,6 @@ % Better Table of contents (Toc), List of figures (Lof), and List of tables (Lot). \usepackage{tocloft} - -% Paragraph section formatting. -\newcommand{\newparagraph}[2][]{ - \ifthenelse { \equal {#1} {} } - { \paragraph{#2}\mbox{} \\} - { \paragraph[#1]{#2}\mbox{} \\ } -} -\newcommand{\newsubparagraph}[2][]{ - \ifthenelse { \equal {#1} {} } - { \subparagraph{#2}\mbox{} \\} - { \subparagraph[#1]{#2}\mbox{} \\ } -} % Hyperlinks. \usepackage[pdftitle={The relax manual}]{hyperref}