Author: bugman
Date: Tue May 13 23:09:09 2014
New Revision: 23159
URL: http://svn.gna.org/viewcvs/relax?rev=23159&view=rev
Log:
Started to create a chapter for the N-state model or ensemble analysis in the
manual.
This simply consists of a few introductory sections and the phathalic acid
graphic.
Added:
trunk/docs/latex/n_state.tex
Modified:
trunk/docs/latex/relax.tex
Added: trunk/docs/latex/n_state.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/n_state.tex?rev=23159&view=auto
==============================================================================
--- trunk/docs/latex/n_state.tex (added)
+++ trunk/docs/latex/n_state.tex Tue May 13 23:09:09 2014
@@ -0,0 +1,85 @@
+% N-state model chapter.
+%%%%%%%%%%%%%%%%%%%%%%%%
+
+\chapter{The N-state model or ensemble analysis} \label{ch: N-state model}
+\index{N-state model|textbf}
+\index{Ensemble analysis|textbf}
+
+
+\begin{figure*}[h]
+ \includegraphics[width=5cm, bb=0 0 1701
1701]{graphics/misc/n_state_model/phthalic_acid_ens_600x600}
+\end{figure*}
+
+
+% Introduction.
+%%%%%%%%%%%%%%%
+
+\section{Introduction to the N-state model}
+
+The modelling of motion in molecules using experimental data consists of
either continuous or discrete distributions.
+These can be visualised respectively as either an infinite number of states
or a limited set of N states.
+The N-state model analysis in relax models the molecular dynamics using an
ensemble of static structures.
+
+This analysis supports a number of data types including:
+\begin{itemize}
+\item Residual dipolar couplings (RDCs)\index{Residual dipolar coupling}
+\item Pseudo-contact shifts (PCSs)\index{Pseudo-contact shifts}
+\item NOEs\index{NOE}
+\end{itemize}
+
+The main idea is to evaluate the quality of a fixed ensemble of structures.
+relax will not perform structural optimisations.
+The evaluation includes:
+\begin{itemize}
+\item Alignment tensor optimisation for the RDCs and PCSs.
+\item Optional optimisation of the position of the paramagnetic centre for
the PCSs.
+\item Calculation of NOE constraint violations.
+\item Q factor calculation for the RDC, PCS, and NOE.
+\end{itemize}
+
+Note that this analysis will also handle single structures.
+Hence you can use the N-state model in relax with N set to 1 to find, for
example, a single alignment tensor for a single structure using RDCs, PCSs,
or both together.
+This is useful for comparing a ensemble to a single structure to determine
if any statistically significant motions are present.
+
+The primary references for the N-state model analysis in relax are:
+\begin{itemize}
+ \item \bibentry{Sun11}
+ \item \bibentry{Erdelyi11}
+\end{itemize}
+
+
+
+% Data types.
+%%%%%%%%%%%%%
+
+\section{Experimental data support for the N-state model}
+
+% RDCs.
+\subsection{RDCs in the N-state model}
+
+Residual dipolar couplings (RDCs)\index{Residual dipolar coupling|textbf}
can be used to evaluate ensembles.
+The ensemble interconversion is assumed to be fast relative to timescale of
the alignment process, hence a single tensor for all members of the ensemble
will be used.
+As such, precise superimposition of structures using a logical frame of
reference is very important.
+This can be performed in relax using the \uf{structure\ufsep{}superimpose}
user function.
+The RDCs can either be from external or internal alignment.
+
+
+% PCSs.
+\subsection{PCSs in the N-state model}
+
+Pseudo-contact shifts (PCSs)\index{Pseudo-contact shifts|textbf} can also be
used to evaluate ensembles.
+The same averaging process as described above for the RDC is assumed.
+Hence correct structural superimposition is essential and one alignment
tensor will be optimised for the entire ensemble.
+
+One powerful feature of relax is that the paramagnetic centre can either be
fixed or be allowed to move during optimisation.
+This allows an unknown paramagnetic centre position to be found.
+Or a known position to be refined to higher accuracy than that possible with
most other techniques.
+
+
+% NOEs.
+\subsection{NOEs in the N-state model}
+
+Another data type which can be used to evaluate dynamics ensembles is the
NOE\index{NOE|textbf}.
+This is not used in optimisation but rather is used to calculate NOE
constraint violations.
+These violations are then compared to evaluate the ensemble.
+In the stereochemistry auto-analysis, these violations will also be
converted to Q factors to allow direct comparison with RDC Q factors.
Modified: trunk/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/relax.tex?rev=23159&r1=23158&r2=23159&view=diff
==============================================================================
--- trunk/docs/latex/relax.tex (original)
+++ trunk/docs/latex/relax.tex Tue May 13 23:09:09 2014
@@ -446,6 +446,7 @@
\include{model-free}
\include{jw_mapping}
\include{consistency_tests}
+\include{n_state}
\include{dispersion}
\part{Power users}
@@ -531,11 +532,13 @@
\index{OpenDX|see{software, OpenDX}}
\index{OpenMPI|see{MPI, OpenMPI}}
\index{OS X|see{Operating system, Mac OS X}}
+\index{PCS|see{Pseudo-contact shift}}
\index{Polak-Ribi\`ere|see{optimisation, algorithm, Polak-Ribi\`ere}}
\index{Polak-Ribi\`ere +|see{optimisation, algorithm, Polak-Ribi\`ere +}}
\index{PyMOL|see{software, PyMOL}}
\index{R1@$\Rone$|see{relaxation rate, spin-lattice}}
\index{R2@$\Rtwo$|see{relaxation rate, spin-spin}}
+\index{RDC|see{Residual dipolar couplings}}
\index{relax|see{software, relax}}
\index{simplex algorithm|see{optimisation, algorithm, Nelder-Mead simplex}}
\index{Sparky|see{software, Sparky}}
r23159 - in /trunk/docs/latex: n_state.tex relax.tex