Author: bugman
Date: Thu Sep 27 10:03:08 2012
New Revision: 17568
URL: http://svn.gna.org/viewcvs/relax?rev=17568&view=rev
Log:
Lots of editing of the model-free GUI section of the user manual.
Modified:
trunk/docs/latex/model-free.tex
Modified: trunk/docs/latex/model-free.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/model-free.tex?rev=17568&r1=17567&r2=17568&view=diff
==============================================================================
--- trunk/docs/latex/model-free.tex (original)
+++ trunk/docs/latex/model-free.tex Thu Sep 27 10:03:08 2012
@@ -1498,17 +1498,17 @@
\newpage
\section{The new protocol in the GUI}
-The model-free analysis can be performed within the GUI (see
Figure~\ref{fig: screenshot: model-free analysis} on page~\pageref{fig:
screenshot: model-free analysis}). This analysis is that of the automated
d'Auvergne protocol. From the analysis wizard (Figure~\ref{fig: screenshot:
analysis wizard} on page~\pageref{fig: screenshot: analysis wizard}), this
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}.
-
-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. Below, a tutorial on
how to use the GUI will be presented with screenshots.
-
-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:
+A model-free analysis can be performed within the GUI (see Figure~\ref{fig:
screenshot: model-free analysis} on page~\pageref{fig: screenshot: model-free
analysis}). This analysis is that of the fully automated d'Auvergne protocol
which can be chosen via the analysis selection wizard (Figure~\ref{fig:
screenshot: analysis wizard} on page~\pageref{fig: screenshot: analysis
wizard}). Please see Section~\ref{sect: new model-free protocol} on
page~\pageref{sect: new model-free protocol} for a description of this new
model-free protocol.
+
+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 returning you warnings if
something is missing. The analysis will only execute once everything is
correctly set up. If this is not the case, clicking on the
\guibutton{Execute relax} button will display a warning window explaining
what the issue is rather than initialising the analysis. Despite the
self-explanatory nature of the GUI a tutorial on how to use the GUI, with
screenshots, will be presented below.
+
+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 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 log}
Note that the size of this \file{log} file could end up being in the
gigabyte range for a model-free analysis.
-For the full analysis to complete, for a protein system this may take
between one to two weeks. 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 (see section~\ref{sect: multi-processor}
on page~\pageref{sect: multi-processor}). 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:
+For the full analysis to complete, for a protein system this may take about
a week. Depending on the nature of the problem and the speed of the
computer, the calculation time may be significantly shorter or longer. 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 (see section~\ref{sect: multi-processor} on page~\pageref{sect:
multi-processor}). For example on a dual-core, dual-CPU 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 --log
log}
@@ -1556,7 +1556,7 @@
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/mf_analysis/about}}
\end{minipage}
-At this point, the results directory where all of the output files and
directories will be saved can be changed.
+At this point, back in the main relax window, the results directory where
all of the output files and directories will be saved can be changed.
% Spin systems.
@@ -1634,7 +1634,7 @@
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/mf_analysis/dipole_wizard_define}}
\end{minipage}
-For this example, directly bonded nitrogens and protons will be analysed.
So firstly the backbone NH pairs will be defined. Leave the values at
\guistring{@N} and \guistring{@H} and click on the \guibutton{Apply} button.
Then change the two spin ID strings to \guistring{@NE1} and \guistring{@HE1}
to set up the tryptophan sidechain indole NH pairs and click on the
\guibutton{Next} button. Note that the regular expression \guistring{@N*}
and \guistring{@H*} should not be used in this first wizard page as otherwise
\prompt{@N} spins will be connected to \prompt{@HE1} spins of the same
tryptophan residue and \prompt{@H} spins to \prompt{@NE1} spins.
+For this example, directly bonded nitrogens and protons will be analysed.
To start with, the backbone NH pairs will be defined. Leave the values at
\guistring{@N} and \guistring{@H} and click on the \guibutton{Apply} button.
Then change the two spin ID strings to \guistring{@NE1} and \guistring{@HE1}
to set up the tryptophan sidechain indole NH pairs and click on the
\guibutton{Next} button. Note that the regular expression \guistring{@N*}
and \guistring{@H*} should not be used in this first wizard page as otherwise
\prompt{@N} spins will be connected to \prompt{@HE1} spins of the same
tryptophan residue and \prompt{@H} spins to \prompt{@NE1} spins.
Now the $\langle r^{-3} \rangle$ averaged distance of 1.02~\AA\ will be set.
Leave all settings as they are and click on \guibutton{Next}:
@@ -1673,9 +1673,9 @@
%~~~~~~~~~~~~~~~~~~~~~~~
\subsection{d'Auvergne protocol GUI mode -- the rest of the setup}
-The local $\tau_m$ models and model-free models should not be modified, the
reason for this is explained in section~\ref{sect: d'Auvergne protocol script
variables} on page~\pageref{sect: d'Auvergne protocol script variables}. The
grid search increments defaults to \guistring{11}. This is used in the
optimisation of the individual model-free models for each spin. This value
should also not be touched unless you know what you are doing (and have read
\citet{dAuvergneGooley08a}). The number of Monte Carlo simulations can be
increase but, for accurate errors estimates, it should not be less than 500
simulations. One additional setting is the \gui{Maximum iterations}. This
is a maximum number of times the protocol will iterate before terminating.
This allows infinite loops to be broken. The value of 30 iterations should
be fine for most analyses.
-
-The \gui{Protocol mode} GUI element setting of \gui{Fully automated} will
not be changed for the analysis of this tutorial. However if you are
studying a system without a 3D structure, you can execute each individual
component of the analysis by clicking on the \guibutton{Change} button. This
will make a window appear:
+The local $\tau_m$ models and model-free models should not be modified, the
reason for this is explained in section~\ref{sect: d'Auvergne protocol script
variables} on page~\pageref{sect: d'Auvergne protocol script variables}. The
grid search increments defaults to \guistring{11}. This is used in the
optimisation of the individual model-free models for each spin. This value
should also not be touched unless you know what you are doing (and have read
\citet{dAuvergneGooley08a}). The number of Monte Carlo simulations can be
increased but, for accurate error estimates, it should not be less than 500
simulations. One additional setting is the \gui{Maximum iterations}. This
is a maximum number of times the protocol will iterate before terminating.
This allows infinite loops to be broken. The value of 30 iterations should
be fine for most analyses.
+
+The \gui{Protocol mode} GUI element setting of \gui{Fully automated} will
not be changed for the analysis of this tutorial. However if you are
studying a system without a 3D structure, you can execute each individual
component of the analysis by clicking on the \guibutton{Change} button. This
will make the protocol mode selection window appear:
\begin{minipage}[h]{\linewidth}
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/mf_analysis/protocol_mode}}
@@ -1696,7 +1696,7 @@
\item Clicking on the \guibutton{relax controller} button on the toolbar.
\end{itemize}
-These messages are very important and will indicate to you if there are any
problems prior to starting the very long model-free calculation. This
information should be stored in the \file{log} file as well. As the
execution of a fully iterative and complete model-free protocol takes a very
long time to finish, it is advisable to save the current relax state. This
will allow you restart the calculation without performing all of the steps
detailed above. There are numerous ways to do this (if this is not enough
for you, please email the relax-users mailing list with your suggestions):
+These messages are very important and will indicate to you if there are any
problems prior to starting the very long model-free calculation. This
information should be stored in the \file{log} file as well. As the
execution of a fully iterative and complete model-free protocol takes a very
long time to finish, it is advisable to save the current relax state. This
will allow you restart the calculation without performing all of the steps
detailed above. Just in case you cannot work out how to do this yourself,
here is a list of the different ways you can do this (if this is not enough
for you, please email the relax-users mailing list with your suggestions):
\begin{itemize}
\item Selecting the \guimenuitemtwo{File}{Save relax state} menu item.
@@ -1706,12 +1706,10 @@
\item Typing \shortcutkey{Shift+Ctrl+S} within the main relax window.
\item Clicking on the \guibutton{Save as} button on the toolbar.
\item Selecting the \guimenuitemthree{User functions}{state}{save} menu item.
-\item Selecting the \guimenuitemthree{User functions}{results}{write} menu
item.
\item Opening up the relax prompt window with \guimenuitemtwo{View}{relax
prompt} or \shortcutkey{Ctrl+P} and using the \uf{state.save} user function.
-\item Opening up the relax prompt window with \guimenuitemtwo{View}{relax
prompt} or \shortcutkey{Ctrl+P} and using the \uf{results.write} user
function.
\end{itemize}
-If all the messages in the relax controller or \file{log} file appear to be
fine and you have saved the current relax state, then you can click on
\guibutton{Execute relax}. This will start the calculations, freeze most of
the GUI and open up the relax controller to give you feedback on the progress
of the calculations:
+If all the messages in the relax controller or \file{log} file appear to be
fine and you have saved the current relax state, then click on
\guibutton{Execute relax}. This will start the calculations, freeze most of
the GUI and open up the relax controller to give you feedback on the progress
of the calculations:
\begin{minipage}[h]{\linewidth}
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/mf_analysis/relax_controller_executing}}
@@ -1739,6 +1737,6 @@
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/mf_analysis/bmrb_export_window}}
\end{minipage}
-From here you can complete the relaxation data metadata if needed, set up
all the molecule information needed for a BMRB deposition, specify the
softwares you have used running up to the model-free analysis and any
spectral processing or relax scripts you have used. You can also add as many
citations relevant to your analysis as you wish. The NMR-STAR formatted file
can be previewed in the relax controller window via the \guibutton{Preview}
button and the final file exported using the \guibutton{Export} button.
-
-Then simply go to the ADIT-NMR webpage at
\href{http://deposit.bmrb.wisc.edu/bmrb-adit/}{http://deposit.bmrb.wisc.edu/bmrb-adit/},
create a new BMRB deposition, upload the file you have created, and
complete the deposition as needed.
+From here you can complete the relaxation data metadata if needed, set up
all the molecule information needed for a BMRB deposition, specify the
softwares you have used running up to the model-free analysis and any
spectral processing or relax scripts you have used. You can also add as many
citations relevant to your analysis as you wish. The NMR-STAR formatted file
can be previewed in the relax controller window via the \guibutton{Preview}
button and the final file created using the \guibutton{Export} button.
+
+Once you are in the stage of writing up, simply go to the ADIT-NMR webpage
at
\href{http://deposit.bmrb.wisc.edu/bmrb-adit/}{http://deposit.bmrb.wisc.edu/bmrb-adit/},
create a new BMRB deposition, upload the file you have created, complete
the deposition as needed, and add the BMRB deposition number to your paper.
r17568 - /trunk/docs/latex/model-free.tex