Author: bugman
Date: Wed May 14 08:48:46 2014
New Revision: 23165
URL: http://svn.gna.org/viewcvs/relax?rev=23165&view=rev
Log:
Exampled the stereochemistry analysis section of the N-state model chapter of
the manual.
Modified:
trunk/docs/latex/infrastruct.tex
trunk/docs/latex/n_state.tex
Modified: trunk/docs/latex/infrastruct.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/infrastruct.tex?rev=23165&r1=23164&r2=23165&view=diff
==============================================================================
--- trunk/docs/latex/infrastruct.tex (original)
+++ trunk/docs/latex/infrastruct.tex Wed May 14 08:48:46 2014
@@ -41,7 +41,7 @@
% relax-users mailing list.
-\subsection{relax-users}
+\subsection{relax-users} \label{sect: relax-users mailing list}
If you would like to ask questions about relax, discuss certain features,
receive help, or to communicate on any other subject related to relax the
mailing list ``relax-users at gna.org''\index{mailing list!relax-users} is
the place to post your message.
To subscribe to the list go to the relax-users information page at
\href{https://mail.gna.org/listinfo/relax-users/}{https://mail.gna.org/listinfo/relax-users/}.
Modified: trunk/docs/latex/n_state.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/n_state.tex?rev=23165&r1=23164&r2=23165&view=diff
==============================================================================
--- trunk/docs/latex/n_state.tex (original)
+++ trunk/docs/latex/n_state.tex Wed May 14 08:48:46 2014
@@ -137,6 +137,8 @@
The following script was used for the analysis in \citet{Sun11}.
It is used to complete the first step of the analysis, the determination of
relative configuration, and for the generation of ensembles for the second
step of the analysis.
+The file is located at
\file{sample\osus{}scripts\ossep{}n\osus{}state\osus{}model\ossep{}stereochem\osus{}analysis.py}.
+The contents of the script are:
\begin{lstlisting}
@@ -251,3 +253,13 @@
)
analysis.run()
\end{lstlisting}
+
+In contrast to all of the other auto-analyses, here you do not set up your
own data pipe containing all of the relevant data that is then passed into
the auto-analysis.
+This may change in the future to allow for more flexibility in how you load
structures, load the RDC and NOE base data, set up pseudo-atoms and bond
lengths for the RDC, etc.
+
+Note that you need to execute this script 6 times, changing the
\pycode{STAGE} variable to match.
+These stages are fully documented at the start of the script.
+
+Due to the original analysis being performed prior to the addition of the
\uf{structure\ufsep{}superimpose} user function to relax, you will see that
the auto-analysis performs superimposition of each ensemble using the
external software \software{Molmol}.
+If you wish to perform this analysis without using \software{Molmol}, please
contact the relax users mailing list ``relax-users at gna.org''\index{mailing
list!relax-users} (see Section~\ref{sect: relax-users mailing list} on
page~\pageref{sect: relax-users mailing list}).
+It would be rather straightforward for the relax developers to replace the
complicated \software{Molmol} superimposition code with a single call to the
\uf{structure\ufsep{}superimpose} user function.
r23165 - in /trunk/docs/latex: infrastruct.tex n_state.tex