Author: bugman
Date: Wed Sep 19 15:42:33 2012
New Revision: 17508
URL: http://svn.gna.org/viewcvs/relax?rev=17508&view=rev
Log:
A number of updates and edits to the intro chapter of the user manual.
The model-free GUI screenshot has been shifted to the intro chapter in
preparation for a full
tutorial with screenshots in the model-free chapter.
Modified:
trunk/docs/latex/intro.tex
trunk/docs/latex/model-free.tex
Modified: trunk/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/intro.tex?rev=17508&r1=17507&r2=17508&view=diff
==============================================================================
--- trunk/docs/latex/intro.tex (original)
+++ trunk/docs/latex/intro.tex Wed Sep 19 15:42:33 2012
@@ -370,7 +370,15 @@
\example{\$ relax your\_script.py}
-You will need to replace \file{your\_script.py} with the name of your
script. An example of a simple script which will minimise the model-free
model ``m4'' after loading six relaxation data sets is
+You will need to replace \file{your\_script.py} with the name of your
script. In most cases you would probably like to keep a log of all of the
messages, warnings and errors relax produces for future reference. To active
logging within relax, type:
+
+\example{\$ relax --log log your\_script.py}
+
+This will place all output (both STDOUT and STDERR) into the \file{log} file
(you can choose any name for this log file). Alternatively you can both log
the output and simultaneously see the messages in your terminal by typing:
+
+\example{\$ relax --tee log your\_script.py}
+
+These command line arguments could be replaced by IO redirection if this is
a familiar concept to you, but note that these arguments are active also in
the GUI mode whereby IO redirection in the terminal will have no effect. An
example of a simple script which will minimise the model-free model ``m4''
after loading six relaxation data sets is
\begin{exampleenv}
\# Create the data pipe. \\
@@ -427,9 +435,7 @@
% Sample scripts.
-%~~~~~~~~~~~~~~~~
-
-\subsection{Sample scripts}
+\subsubsection{Sample scripts}
\index{scripting!sample scripts}
A few sample scripts have been provided in the directory
\directory{sample\_scripts}. These can be copied and modified for different
types of data analysis.
@@ -481,7 +487,7 @@
\caption[GUI screenshot -- $\Rtwo$ analysis]{Screenshot of the relax GUI
interface -- the $\Rtwo$ analysis.}\label{fig: screenshot: R2 analysis}
\end{figure}
-If the wx Python module is installed on your system, you will have access to
the GUI interface of relax. To launch relax in GUI mode, type either
+If the wxPython module is installed on your system, you will have access to
the GUI interface of relax. To launch relax in GUI mode, type either
\example{\$ relax -g}
@@ -489,7 +495,19 @@
\example{\$ relax --gui}
-The GUI is still in development, so many of the features of the
prompt/scripting user interfaces are not available (however the prompt and
script modes can be accessed through the menus if needed). Currently the GUI
is an interface to the automatic analyses. This provides an easy way for the
user to perform quick analyses. The interface consists of a tab for each
analysis. By clicking on the \guimenuitemtwo{File}{New analysis} menu entry,
the analysis wizard will appear (see Figure~\ref{fig: screenshot: analysis
wizard}). The following analyses can be set up using this wizard:
+In most cases you will probably like to have a permanent copy of all the
messages, warnings, and errors relax produces for future reference. In such
a case you could run the GUI with:
+
+\example{\$ relax --gui --log log}
+
+This will place all of the output into the \file{log} file.
+
+% Model-free analysis screenshot
+\begin{figure}
+\centerline{\includegraphics[width=\textwidth, bb=14 14 1065
768]{graphics/screenshots/analysis_mf.eps.gz}}
+\caption[GUI screenshot -- Model-free analysis]{Screenshot of the relax GUI
interface -- the automated model-free analysis. The analysis is fully
automated via a new model-free protocol as described in detail in
Chapter~\ref{ch: model-free}. Clicking on the \guibutton{About} button in
the bottom left hand corner will give a full description of the protocol.
For using this interface or any of the modern-day model-free protocols, data
from at least two magnetic field strengths must be without question
collected.}\label{fig: screenshot: model-free analysis}
+\end{figure}
+
+The GUI is currently and interface to the automatic analyses, providing an
easy way to perform quick analyses. The interface consists of a tab for each
analysis. By clicking on the \guimenuitemtwo{File}{New analysis} menu entry
or the \guibutton{New analysis} toolbar button, the analysis wizard will
appear (see Figure~\ref{fig: screenshot: analysis wizard}). The following
analyses can be set up using this wizard:
\begin{description}
\item[Steady-state NOE:] this provides access to the steady-state NOE
calculation with pseudo Monte Carlo simulations for error analysis (this
falls back to bootstrapping as this is a calculation rather than
optimisation). See Figure~\ref{fig: screenshot: NOE analysis} on
page~\pageref{fig: screenshot: NOE analysis}.
@@ -593,7 +611,7 @@
If you have access to a 256 node cluster and can run calculations on all
nodes, assuming that the \file{dauvergne\_protocol.py} automated model-free
analysis sample script will be used (after modification for the system under
study), relax can be executed by typing:
-\example{\$ mpirun -np 257 /usr/local/bin/relax --multi=`mpi4py'
dauvergne\_protocol.py}
+\example{\$ mpirun -np 257 /usr/local/bin/relax --multi=`mpi4py' --log log
dauvergne\_protocol.py}
Note that the argument \prompt{-np} value is one more than the number of
slaves you would like to run. You should then see the following text in the
initial relax printout:
Modified: trunk/docs/latex/model-free.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/model-free.tex?rev=17508&r1=17507&r2=17508&view=diff
==============================================================================
--- trunk/docs/latex/model-free.tex (original)
+++ trunk/docs/latex/model-free.tex Wed Sep 19 15:42:33 2012
@@ -1342,12 +1342,6 @@
\section{The GUI auto-analysis}
-% Model-free analysis screenshot
-\begin{figure}
-\centerline{\includegraphics[width=\textwidth, bb=14 14 1065
768]{graphics/screenshots/analysis_mf.eps.gz}}
-\caption[GUI screenshot -- Model-free analysis]{Screenshot of the relax GUI
interface -- the automated model-free analysis. The analysis is fully
automated via a new model-free protocol as described in detail in
Chapter~\ref{ch: model-free}. Clicking on the \guibutton{About} button in
the bottom left hand corner will give a full description of the protocol.
For using this interface or any of the modern-day model-free protocols, data
from at least two magnetic field strengths must be without question
collected.}\label{fig: screenshot: model-free analysis}
-\end{figure}
-
From the analysis wizard (Figure~\ref{fig: screenshot: analysis wizard} on
page~\pageref{fig: screenshot: analysis wizard}), the automated model-free
analysis can be selected. This analysis will use the new model-free protocol
described in Section~\ref{sect: new model-free protocol} on
page~\pageref{sect: new model-free protocol}. Once the analysis is
initialised, the screen should look like Figure~\ref{fig: screenshot:
model-free analysis}. The \guibutton{About} button in the bottom left will
bring up a window with the same description as given in the sample script.
After reading this chapter, the use of this GUI analysis should be self
explanatory (if not, then please consider filing a bug report at
\href{https://gna.org/bugs/?func=additem\&group=relax}{https://gna.org/bugs/?func=additem\&group=relax}
or a support request at
\href{https://gna.org/support/?func=additem\&group=relax}{https://gna.org/support/?func=additem\&group=relax}).
The GUI is designed to be robust -- you should be able to set up all the
input data and parameters in any order, with relax giving warning is
something is missing. The analysis will only execute once everything is
correctly set up. If this is not the case, rather than starting the
analysis, clicking on the \guibutton{Execute relax} button will warn about
the incorrect set up, describing what the problem is.
If the \gui{Protocol mode} field is left to the \gui{Fully automated}
setting then, after clicking on \guibutton{Execute relax}, the calculation
can be left for one to two weeks to complete. It is highly recommended to
check the log messages in the relax controller window, at least at the start
of the analysis, to make sure that all the data is being read correctly and
everything is set up as desired. All warnings should be carefully checked as
these can indicate a fatal problem. If you would like to log all the
messages into a file, relax can be run with:
r17508 - in /trunk/docs/latex: intro.tex model-free.tex