Author: bugman
Date: Wed Nov 6 15:39:29 2013
New Revision: 21398
URL: http://svn.gna.org/viewcvs/relax?rev=21398&view=rev
Log:
Rearranged the sections of the dispersion chapter of the manual.
Modified:
branches/relax_disp/docs/latex/dispersion.tex
Modified: branches/relax_disp/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion.tex?rev=21398&r1=21397&r2=21398&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion.tex (original)
+++ branches/relax_disp/docs/latex/dispersion.tex Wed Nov 6 15:39:29 2013
@@ -804,6 +804,83 @@
+% TODO.
+%%%%%%%
+
+\section{To do -- dispersion features yet to be implemented}
+\label{sect: dispersion: TODO}
+
+The capabilities of the relaxation dispersion analysis in relax is expansive
but it cannot be called complete.
+There are a number of features and models yet to be implemented.
+Missing features include:
+\begin{itemize}
+\item The handling of off-resonance effects in the models of the numeric
solution for CPMG-type data.
+This is specifically the `NS CPMG 2-site 3D' and `NS CPMG 2-site star'
models and their `* full' equivalents.
+The necessary infrastructure is in place, but not activated yet (mainly due
to a lack of synthetic data to test against).
+\item Multi-state data -- the handling of data from two sets of peaks from
the same spin system is not properly supported.
+It is currently handled by assuming each state is a separate spin system but
this means that $\dw$, $\dwH$ and related parameters are not shared as they
should be.
+\item The van't Hoff analysis of multi-temperature dispersion data (see
\url{https://en.wikipedia.org/wiki/Van\_\%27t\_Hoff\_equation}).
+\item ZZ exchange.
+\item HD exchange.
+\end{itemize}
+
+If you would like one of these features, please contact the ``relax-devel at
gna.org''\index{mailing list!relax-devel} mailing list.
+The most useful would be if you have synthetic data whereby you know what
the true solution should be.
+This can then be incorporated into a relax system test and the feature
implemented to allow the test to pass.
+Note that such data should never be emailed to a public mailing list!
+Synthetic data, or experimental data, can be obtained from the literature.
+
+Some of the missing models include:
+\begin{description}
+\item[`NS $\Ronerho$ 3-site':]\index{relaxation dispersion!NS R1rho 3-site
model} The model of the numeric solution for 3-site exchange for
$\Ronerho$-type data.
+\item[`MMQ 3-site':]\index{relaxation dispersion!MMQ 3-site model} The
model of the numeric solution for 3-site exchange for multiple quantum
CPMG-type data. This is the linear 3-site exchange model.
+\item[`MMQ 3-site branched':]\index{relaxation dispersion!MMQ 3-site
branched model} Similar to the `MMQ 3-site' but with one of the $\kex$
parameters not set to zero.
+\end{description}
+
+Information for how these can be added is given in the next section.
+
+
+% Tutorial - adding models.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{Tutorial for adding relaxation dispersion models}
+\label{sect: dispersion: model tutorial}
+
+As the field of NMR relaxation dispersion has a very long history, it is not
possible to include all analytic and numeric relaxation dispersion models for
both CPMG-type\index{relaxation dispersion!CPMG-type experiment} or
$\Ronerho$-type\index{relaxation dispersion!$\Ronerho$-type experiment}
experiments in relax. However it is not too difficult to add new models for
your own needs if you have some Python, Matlab, Mathematica, or similar
scripting skills. The steps required are detailed on the
\href{http://wiki.nmr-relax.com/}{relax wiki} page
\url{http://wiki.nmr-relax.com/Tutorial\_for\_adding\_relaxation\_dispersion\_models\_to\_relax}.
+
+
+% Software comparison.
+%%%%%%%%%%%%%%%%%%%%%%
+
+\section{Comparison of dispersion analysis software}
+\label{sect: dispersion: software comparison}
+
+Diverse software exists for analysing relaxation dispersion data.
+The following is a list of the officially released software which you can
use instead of relax:
+
+\begin{description}
+\item[CPMGFit] Art Palmer's original dispersion analysis software at
\url{http://www.palmer.hs.columbia.edu/software/cpmgfit.html}.
+\item[cpmg\_fit] Dmitry Korzhnev's dispersion software available upon
request.
+\item[CATIA] Flemming Hansen's dispersion software at
\url{http://www.biochem.ucl.ac.uk/hansen/catia/}. The reference is
\citet{Hansen08}.
+\item[NESSY] Michael Bieri's dispersion software at
\url{http://home.gna.org/nessy/}. The reference is \citet{BieriGooley11}.
+\item[GUARDD] Ian Kleckner's dispersion software at
\url{http://code.google.com/p/guardd/}. The reference is
\citet{KlecknerFoster12}.
+\item[ShereKhan] See the web server at \url{http://sherekhan.bionmr.org/}.
The reference is \citet{Mazur13}.
+\item[GLOVE] Peter Wright's dispersion software at
\url{http://www.scripps.edu/wright/}. The reference is \citet{Sugase13}.
+\item[chemex] Guillaume Bouvignies' dispersion software which can be found
at \url{http://code.google.com/p/chemex/}.
+\end{description}
+
+There is currently support in relax for generating the input files for
CPMGFit, CATIA, NESSY, and ShereKhan and for running CPMGFit and CATIA from
within relax.
+
+The features of the different software are compared in Table~\ref{table:
dispersion software} on page~\pageref{table: dispersion software}.
+Note that this table is likely to be incomplete so please see the websites
of the respective software for an up to date list of features.
+The aim of this table is to provide a fair comparison between all of the
available dispersion software.
+Therefore if you do find deficiencies or errors in this table please report
these either to the relax users mailing list at ``relax-users at
gna.org''\index{mailing list!relax-users}, submit a bug
report\index{bug!report} (see section~\ref{reporting bugs} on
page~\pageref{reporting bugs}), or send a private message to one of the relax
developers (\url{http://gna.org/project/memberlist.php?group=relax}) so that
the details can be corrected.
+
+\clearpage
+\input{dispersion_software}
+
+
+
% Script UI.
%%%%%%%%%%%%
@@ -1268,80 +1345,3 @@
This will start the auto-analysis.
If you are adventurous, you can replace this line with your own
\uf{grid\_search}, \uf{minimise}, and \uf{monte\_carlo.*} user function calls
and design your own protocol.
For ideas in designing your own advanced analysis, see the
\file{auto\_analysis/\linebreak[0]{}relax\_disp.py} file.
-
-
-
-% TODO.
-%%%%%%%
-
-\section{To do -- dispersion features yet to be implemented}
-\label{sect: dispersion: TODO}
-
-The capabilities of the relaxation dispersion analysis in relax is expansive
but it cannot be called complete.
-There are a number of features and models yet to be implemented.
-Missing features include:
-\begin{itemize}
-\item The handling of off-resonance effects in the models of the numeric
solution for CPMG-type data.
-This is specifically the `NS CPMG 2-site 3D' and `NS CPMG 2-site star'
models and their `* full' equivalents.
-The necessary infrastructure is in place, but not activated yet (mainly due
to a lack of synthetic data to test against).
-\item Multi-state data -- the handling of data from two sets of peaks from
the same spin system is not properly supported.
-It is currently handled by assuming each state is a separate spin system but
this means that $\dw$, $\dwH$ and related parameters are not shared as they
should be.
-\item The van't Hoff analysis of multi-temperature dispersion data (see
\url{https://en.wikipedia.org/wiki/Van\_\%27t\_Hoff\_equation}).
-\item ZZ exchange.
-\item HD exchange.
-\end{itemize}
-
-If you would like one of these features, please contact the ``relax-devel at
gna.org''\index{mailing list!relax-devel} mailing list.
-The most useful would be if you have synthetic data whereby you know what
the true solution should be.
-This can then be incorporated into a relax system test and the feature
implemented to allow the test to pass.
-Note that such data should never be emailed to a public mailing list!
-Synthetic data, or experimental data, can be obtained from the literature.
-
-Some of the missing models include:
-\begin{description}
-\item[`NS $\Ronerho$ 3-site':]\index{relaxation dispersion!NS R1rho 3-site
model} The model of the numeric solution for 3-site exchange for
$\Ronerho$-type data.
-\item[`MMQ 3-site':]\index{relaxation dispersion!MMQ 3-site model} The
model of the numeric solution for 3-site exchange for multiple quantum
CPMG-type data. This is the linear 3-site exchange model.
-\item[`MMQ 3-site branched':]\index{relaxation dispersion!MMQ 3-site
branched model} Similar to the `MMQ 3-site' but with one of the $\kex$
parameters not set to zero.
-\end{description}
-
-Information for how these can be added is given in the next section.
-
-
-% Tutorial - adding models.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\section{Tutorial for adding relaxation dispersion models}
-\label{sect: dispersion: model tutorial}
-
-As the field of NMR relaxation dispersion has a very long history, it is not
possible to include all analytic and numeric relaxation dispersion models for
both CPMG-type\index{relaxation dispersion!CPMG-type experiment} or
$\Ronerho$-type\index{relaxation dispersion!$\Ronerho$-type experiment}
experiments in relax. However it is not too difficult to add new models for
your own needs if you have some Python, Matlab, Mathematica, or similar
scripting skills. The steps required are detailed on the
\href{http://wiki.nmr-relax.com/}{relax wiki} page
\url{http://wiki.nmr-relax.com/Tutorial\_for\_adding\_relaxation\_dispersion\_models\_to\_relax}.
-
-
-% Software comparison.
-%%%%%%%%%%%%%%%%%%%%%%
-
-\section{Comparison of dispersion analysis software}
-\label{sect: dispersion: software comparison}
-
-Diverse software exists for analysing relaxation dispersion data.
-The following is a list of the officially released software which you can
use instead of relax:
-
-\begin{description}
-\item[CPMGFit] Art Palmer's original dispersion analysis software at
\url{http://www.palmer.hs.columbia.edu/software/cpmgfit.html}.
-\item[cpmg\_fit] Dmitry Korzhnev's dispersion software available upon
request.
-\item[CATIA] Flemming Hansen's dispersion software at
\url{http://www.biochem.ucl.ac.uk/hansen/catia/}. The reference is
\citet{Hansen08}.
-\item[NESSY] Michael Bieri's dispersion software at
\url{http://home.gna.org/nessy/}. The reference is \citet{BieriGooley11}.
-\item[GUARDD] Ian Kleckner's dispersion software at
\url{http://code.google.com/p/guardd/}. The reference is
\citet{KlecknerFoster12}.
-\item[ShereKhan] See the web server at \url{http://sherekhan.bionmr.org/}.
The reference is \citet{Mazur13}.
-\item[GLOVE] Peter Wright's dispersion software at
\url{http://www.scripps.edu/wright/}. The reference is \citet{Sugase13}.
-\item[chemex] Guillaume Bouvignies' dispersion software which can be found
at \url{http://code.google.com/p/chemex/}.
-\end{description}
-
-There is currently support in relax for generating the input files for
CPMGFit, CATIA, NESSY, and ShereKhan and for running CPMGFit and CATIA from
within relax.
-
-The features of the different software are compared in Table~\ref{table:
dispersion software} on page~\pageref{table: dispersion software}.
-Note that this table is likely to be incomplete so please see the websites
of the respective software for an up to date list of features.
-The aim of this table is to provide a fair comparison between all of the
available dispersion software.
-Therefore if you do find deficiencies or errors in this table please report
these either to the relax users mailing list at ``relax-users at
gna.org''\index{mailing list!relax-users}, submit a bug
report\index{bug!report} (see section~\ref{reporting bugs} on
page~\pageref{reporting bugs}), or send a private message to one of the relax
developers (\url{http://gna.org/project/memberlist.php?group=relax}) so that
the details can be corrected.
-
-\clearpage
-\input{dispersion_software}
r21398 - /branches/relax_disp/docs/latex/dispersion.tex