Author: bugman
Date: Fri Apr 27 12:30:01 2012
New Revision: 15844
URL: http://svn.gna.org/viewcvs/relax?rev=15844&view=rev
Log:
Added GUI sections to the end of the NOE, R1+R2 and model-free chapters of
the user manual.
The screenshots of each of the GUI analyses have been shifted into the
specific analysis chapters.
Modified:
1.3/docs/latex/curvefit.tex
1.3/docs/latex/intro.tex
1.3/docs/latex/model-free.tex
1.3/docs/latex/noe.tex
Modified: 1.3/docs/latex/curvefit.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/curvefit.tex?rev=15844&r1=15843&r2=15844&view=diff
==============================================================================
--- 1.3/docs/latex/curvefit.tex (original)
+++ 1.3/docs/latex/curvefit.tex Fri Apr 27 12:30:01 2012
@@ -216,3 +216,24 @@
and finally the program state is saved for future reference
\example{state.save(file=`rx.save', force=True)}
+
+
+
+% GUI.
+%%%%%%
+
+\section{The GUI auto-analysis}
+
+The $\Rone$ and $\Rtwo$ relaxation rates can be calculated using the relax
GUI (see Figures~\ref{fig: screenshot: R1 analysis} and~\ref{fig: screenshot:
R1 analysis}). These auto-analyses can be selected using the analysis
selection wizard (Figure~\ref{fig: screenshot: analysis wizard} on
page~\pageref{fig: screenshot: analysis wizard}). Just as with the
steady-state NOE, these auto-analyses are very similar in spirit to the
sample script described in this chapter, though the Grace 2D visualisation is
more advanced. If you have read this chapter, the usage of these analyses
should be self explanatory.
+
+% R1 analysis screenshot
+\begin{figure}
+\centerline{\includegraphics[width=\textwidth, bb=14 14 1065
768]{graphics/screenshots/analysis_r1.eps.gz}}
+\caption[GUI screenshot -- $\Rone$ analysis]{Screenshot of the relax GUI
interface -- the $\Rone$ analysis.}\label{fig: screenshot: R1 analysis}
+\end{figure}
+
+% R2 analysis screenshot
+\begin{figure}
+\centerline{\includegraphics[width=\textwidth, bb=14 14 1065
768]{graphics/screenshots/analysis_r2.eps.gz}}
+\caption[GUI screenshot -- $\Rtwo$ analysis]{Screenshot of the relax GUI
interface -- the $\Rtwo$ analysis.}\label{fig: screenshot: R2 analysis}
+\end{figure}
Modified: 1.3/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/intro.tex?rev=15844&r1=15843&r2=15844&view=diff
==============================================================================
--- 1.3/docs/latex/intro.tex (original)
+++ 1.3/docs/latex/intro.tex Fri Apr 27 12:30:01 2012
@@ -340,12 +340,6 @@
\caption[GUI screenshot -- Analysis wizard screenshot]{Screenshot of the
relax GUI interface -- the analysis selection wizard. From here, the
steady-state NOE analysis, the $\Rone$ and $\Rtwo$ relaxation rates via
exponential curve-fitting, and the automated model-free analysis can be
selected.}\label{fig: screenshot: analysis wizard}
\end{figure}
-% NOE analysis screenshot
-\begin{figure}
-\centerline{\includegraphics[width=0.9\textwidth, bb=14 14 1065
768]{graphics/screenshots/analysis_noe.eps.gz}}
-\caption[GUI screenshot -- NOE analysis]{Screenshot of the relax GUI
interface -- the steady-state NOE analysis.}\label{fig: screenshot: NOE
analysis}
-\end{figure}
-
% Scripting.
@@ -403,25 +397,6 @@
Scripting is much more powerful than the prompt as advanced
Python\index{Python} programming can be employed (see the file
`relax\_curve\_diff.py' in the `sample\_scripts' directory for an example).
-% R1 analysis screenshot
-\begin{figure}
-\centerline{\includegraphics[width=0.9\textwidth, bb=14 14 1065
768]{graphics/screenshots/analysis_r1.eps.gz}}
-\caption[GUI screenshot -- $\Rone$ analysis]{Screenshot of the relax GUI
interface -- the $\Rone$ analysis.}\label{fig: screenshot: R1 analysis}
-\end{figure}
-
-% R2 analysis screenshot
-\begin{figure}
-\centerline{\includegraphics[width=0.9\textwidth, bb=14 14 1065
768]{graphics/screenshots/analysis_r2.eps.gz}}
-\caption[GUI screenshot -- $\Rtwo$ analysis]{Screenshot of the relax GUI
interface -- the $\Rtwo$ analysis.}\label{fig: screenshot: R2 analysis}
-\end{figure}
-
-% Model-free analysis screenshot
-\begin{figure}
-\centerline{\includegraphics[width=0.9\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 `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}
-
-
% Sample scripts.
%~~~~~~~~~~~~~~~~
@@ -460,9 +435,9 @@
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 \texttt{`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:
\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}.
-\item[$\Rone$ and $\Rtwo$]: these provide easy access to optimisations and
error analysis for the $\Rone$ and $\Rtwo$ relaxation rates via exponential
curve-fitting (see Figures~\ref{fig: screenshot: R1 analysis} and~\ref{fig:
screenshot: R2 analysis}).
-\item[Model-free analysis]: A fully automatic model-free protocol is
provided in another tab. This operates via the \texttt{dauvergne\_protocol}
module which implements the protocol of \cite{dAuvergneGooley08b} (see
Figure~\ref{fig: screenshot: model-free analysis}).
+\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}.
+\item[$\Rone$ and $\Rtwo$]: these provide easy access to optimisations and
error analysis for the $\Rone$ and $\Rtwo$ relaxation rates via exponential
curve-fitting (see Figures~\ref{fig: screenshot: R1 analysis} and~\ref{fig:
screenshot: R2 analysis} on pages~\pageref{fig: screenshot: R1 analysis}
and~\pageref{fig: screenshot: R2 analysis}).
+\item[Model-free analysis]: A fully automatic model-free protocol is
provided in another tab. This operates via the \texttt{dauvergne\_protocol}
module which implements the protocol of \cite{dAuvergneGooley08b} (see
Figure~\ref{fig: screenshot: model-free analysis} on page~\pageref{fig:
screenshot: model-free analysis}).
\end{description}
A number of windows in the GUI provide user feedback or allow for the
viewing and editing of data. These include:
Modified: 1.3/docs/latex/model-free.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/model-free.tex?rev=15844&r1=15843&r2=15844&view=diff
==============================================================================
--- 1.3/docs/latex/model-free.tex (original)
+++ 1.3/docs/latex/model-free.tex Fri Apr 27 12:30:01 2012
@@ -979,6 +979,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{The new model-free optimisation protocol}
+\label{sect: new model-free protocol}
% The model-free models.
%~~~~~~~~~~~~~~~~~~~~~~~
@@ -1285,3 +1286,34 @@
The initialisation of data in this script is almost identical to that of the
sample script for a single model free model in section~\ref{sect: single mf
model} on page~\pageref{sect: single mf model}. Once the data is set up,
then the data pipe as well as a number of user defined variables are passed
into the \texttt{`dAuvergne\_protocol'} class. This script needs to be
executed multiple times for each of the diffusion models.
For a full analysis of a protein system, the analysis may require between
one to two weeks to complete. The analysis is performed as described in the
previous sections and summarised in Figure~\ref{fig: new protocol}. If you
are curious, the implementation is within a very large relax script found at
\texttt{`auto\_analyses/dauvergne\_protocol.py'} (which must never be
changed). This auto-analyses script hides all of the complexity of the
analysis from the sample script.
+
+
+
+% GUI.
+%%%%%%
+
+\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 `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 `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 `Execute relax' button will warn about the
incorrect set up, describing what the problem is.
+
+If the `Protocol mode' field is left to the `Fully automated' setting then,
after clicking on `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:
+
+\example{\$ relax -g --log my.log}
+
+Note that the size of this log file could end up being in the gigabyte range
for a model-free analysis. To speed up the calculations, if you have access
to multiple cores and/or hyper-threading, the GUI can be run using Gary
Thompson's multi-processor framework. For example on a dual-CPU with
dual-core system, four calculations can be run simultaneously. In this case,
the GUI can be launched with:
+
+\example{\$ mpirun -np 5 /usr/local/bin/relax --multi=`mpi4py' --gui}
+
+This assumes that OpenMPI and the Python mpi4py module have been installed
on your system. If this is successful, you should only see a single relax
GUI window (and not five windows) and in the relax controller, you should see
text similar to:
+
+\example{Processor fabric: MPI 2.1 running via mpi4py with 4 slave
processors \& 1 master. Using Open MPI 1.4.3.}
+
+If you are using a different MPI implementation, please see the
documentation of that implementation to see how to launch a program in MPI
mode.
+
+Upon completion of the analysis, the save and results files for the final
result will be located in the \texttt{`final'} directory within the selected
results directory. The results files will consist of text files for each of
the spin specific model-free parameters, 2D Grace plots of the model-free
parameters, PyMOL and MOLMOL macros for superimposing the model-free
parameter values onto the 3D structure of the molecule, and a PDB
representation of the final diffusion tensor. Further visualisations of the
results are possible via the \texttt{`User functions'} menu entry. For
example to generate a 2D plot of order parameters for one of the other
diffusion tensor results, the pipe editor window can be used to switch data
pipes to the other diffusion models and then the \texttt{`User
functions->grace->write'} menu item can be selected to create the plot.
Modified: 1.3/docs/latex/noe.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/noe.tex?rev=15844&r1=15843&r2=15844&view=diff
==============================================================================
--- 1.3/docs/latex/noe.tex (original)
+++ 1.3/docs/latex/noe.tex Fri Apr 27 12:30:01 2012
@@ -235,3 +235,18 @@
\centerline{\includegraphics[width=0.8\textwidth, bb=0 0 792
612]{images/noe.eps.gz}}
\caption[NOE plot]{A Grace\index{software!Grace|textbf} plot of the NOE
value and error against the residue number. This is an example of the output
of the user function \texttt{grace.write()}.}\label{fig: NOE plot}
\end{figure}
+
+
+
+% GUI.
+%%%%%%
+
+\section{The GUI auto-analysis}
+
+The relax graphical user interface provides access to an automated
steady-state NOE analysis (Figure~\ref{fig: screenshot: NOE analysis}). This
can be selected through the analysis selection wizard, see Figure~\ref{fig:
screenshot: analysis wizard} on page~\pageref{fig: screenshot: analysis
wizard}. This auto-analysis operates in the same way as the sample script
described in this chapter. The 2D Grace visualisation will also be created
as part of the analysis and presented in the results viewer window
(Figure~\ref{fig: screenshot: results viewer} on page~\pageref{fig:
screenshot: results viewer}).
+
+% NOE analysis screenshot
+\begin{figure}
+\centerline{\includegraphics[width=\textwidth, bb=14 14 1065
768]{graphics/screenshots/analysis_noe.eps.gz}}
+\caption[GUI screenshot -- NOE analysis]{Screenshot of the relax GUI
interface -- the steady-state NOE analysis.}\label{fig: screenshot: NOE
analysis}
+\end{figure}
r15844 - in /1.3/docs/latex: curvefit.tex intro.tex model-free.tex noe.tex