r27888 - in /branches/frame_order_cleanup/docs/latex: frame_order.tex frame_order/introduction.tex -- September 29, 2015 - 16:02

Author: bugman
Date: Tue Sep 29 16:02:20 2015
New Revision: 27888

URL: http://svn.gna.org/viewcvs/relax?rev=27888&view=rev
Log:
Added an introduction for the frame order chapter of the manual.


Added:
    branches/frame_order_cleanup/docs/latex/frame_order/introduction.tex
Modified:
    branches/frame_order_cleanup/docs/latex/frame_order.tex

Modified: branches/frame_order_cleanup/docs/latex/frame_order.tex
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/latex/frame_order.tex?rev=27888&r1=27887&r2=27888&view=diff
==============================================================================
--- branches/frame_order_cleanup/docs/latex/frame_order.tex     (original)
+++ branches/frame_order_cleanup/docs/latex/frame_order.tex     Tue Sep 29 
16:02:20 2015
@@ -6,6 +6,7 @@
 
 
 % The sections.
+\input{frame_order/introduction}
 \input{frame_order/theory}
 \input{frame_order/modelling}
 \input{frame_order/pcs_numerical_integration}

Added: branches/frame_order_cleanup/docs/latex/frame_order/introduction.tex
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/latex/frame_order/introduction.tex?rev=27888&view=auto
==============================================================================
--- branches/frame_order_cleanup/docs/latex/frame_order/introduction.tex      
  (added)
+++ branches/frame_order_cleanup/docs/latex/frame_order/introduction.tex      
  Tue Sep 29 16:02:20 2015
@@ -0,0 +1,40 @@
+% Frame order introduction.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{Introduction}
+
+
+
+% Tensors of frame ordering.
+%~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{Tensors of frame ordering}
+
+The frame order theory is a new analysis type designed for studying the 
rigid body motions of molecules.
+It provides a bridge between statistical mechanical molecular dynamics (MD) 
models and all rotational molecular physics techniques, by defining a series 
of rank-$2n$ frame order tensors.
+These tensors define the maximum information content of a rotational 
molecular physics experiment, as well as what type of information is 
contained in the data.
+To use the frame order theory, two steps are required:
+\begin{enumerate}
+\item The physics of the experiment should be decomposed into statistically 
mechanically averaged product of rotation matrix elements.
+\item The MD model should be expressed in terms of a rotation matrix which 
modulates the motion of the rigid body, within the reference frame matching 
that of the experimental data.
+\end{enumerate}
+
+
+
+
+% RDC and PCS data.
+%~~~~~~~~~~~~~~~~~~
+
+\subsection{Ln$^{3+}$ aligned RDC and PCS data}
+
+For the current implementation in relax, the frame order theory has been 
derived for molecules internally aligned using paramagnetic lanthanide ions.
+The data required for the analysis includes both residual dipolar couplings 
(RDCs) and pseudocontact shifts (PCSs).
+Both data sets are required as they are complementary, each carrying 
different dynamics information:
+\begin{description}
+\item[RDCs:]  This data is dominated by the amplitudes of the MD motions, 
and the orientation of the statical mechanical average structure.
+\item[PCSs:]  These mainly provide information about the directions of the 
MD motions, and the orientation and position of the statical mechanical 
average structure.
+\end{description}
+
+For a successful analysis, the data must be of the highest quality.
+In addition, multiple alignments are required, either using different 
lanthanide ions and/or a different attachment point for the lanthanide ion.
+Note that the current implementation only handles alignment of one rigid 
body or domain.