Author: bugman
Date: Tue Feb 25 17:54:57 2014
New Revision: 22317
URL: http://svn.gna.org/viewcvs/relax?rev=22317&view=rev
Log:
Completed the tutorial for using the dispersion analysis in the GUI.
This is for the relaxation dispersion chapter of the manual.
Modified:
trunk/docs/latex/dispersion.tex
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=22317&r1=22316&r2=22317&view=diff
==============================================================================
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Tue Feb 25 17:54:57 2014
@@ -2598,10 +2598,6 @@
\example{\$ relax --help}
-In this example, Gary Thompson's multiprocessor framework (see
section~\ref{sect: Relaxation dispersion using OpenMPI} on
page~\pageref{sect: Relaxation dispersion using OpenMPI}) will be used with
OpenMPI on a single four-core, hyper-threaded computer with the command:
-
-\example{\$ mpirun -np 8 /data/relax/relax-trunk/relax --multi='mpi4py'
--log $\sim$/tmp/dispersion/log\_non\_clustered --gui}
-
% Two analyses.
%~~~~~~~~~~~~~~
@@ -2614,6 +2610,13 @@
This will use model selection to determine if any statistically
significant relaxation dispersion is present by comparing to the `No Rex'
dispersion model.
\item The second analysis will consists of clustering spins with similar
kinetics and thermodynamics parameters (exchange rates and populations
respectively) and optimising these clusters using a common set of exchange
parameters.
\end{itemize}
+
+In this example, Gary Thompson's multiprocessor framework (see
section~\ref{sect: Relaxation dispersion using OpenMPI} on
page~\pageref{sect: Relaxation dispersion using OpenMPI}) will be used with
OpenMPI on a single four-core, hyper-threaded computer with the command:
+
+\example{\$ mpirun -np 8 /data/relax/relax-trunk/relax --multi='mpi4py'
--log $\sim$/tmp/dispersion/log\_non\_clustered --gui}
+
+A different command will be used for the clustered analysis to store the log
messages in a separate file.
+The logs will be used in the end to compare the two analysis types.
% Initialisation of the data pipe.
@@ -2975,7 +2978,7 @@
Change the frequency to 800.0 MHz and continue for the next set of matching
spectrum IDs.
Finally click on \guibutton{Next} to move to the next wizard page.
If you have not used the exact values from the files, the relax controller
window will appear with the warning:
-\begin{lstlisting}[numbers=none]
+\begin{lstlisting}[language=relax_log,numbers=none]
relax> spectrometer.frequency(id='500_reference', frq=500.0, units='MHz')
RelaxWarning: The precise spectrometer frequency should be suppled, a value
such as 500000000 or 5e8 for a 500 MHz machine is not acceptable. Please see
the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in
the Bruker acqus file.
\end{lstlisting}
@@ -3138,7 +3141,7 @@
Firstly, to see which models have been chosen for the spin systems and which
have no statistically significant dispersion, find the \file{model.out} file
and double click on it.
You should see the following:
-\begin{lstlisting}[basicstyle=\scriptsize,numbers=none]
+\begin{lstlisting}[basicstyle=\ttfamily \scriptsize,numbers=none]
# Parameter description: The dispersion model.
#
# mol_name res_num res_name spin_num spin_name value
error
@@ -3255,7 +3258,7 @@
To improve the appearance of this plot, please refer to the Grace software
documentation.
-% comparing models.
+% Comparing models.
%~~~~~~~~~~~~~~~~~~
\subsection{Dispersion GUI mode -- comparing models}
@@ -3283,10 +3286,17 @@
\subsection{Dispersion GUI mode -- the clustered analysis}
+Before this second analysis will be performed, the relax state will be saved
in the file \file{state.bz2} and the program closed.
+Then to store the details of the second analysis, relax will be restarted
with the command:
+
+\example{\$ mpirun -np 8 /data/relax/relax-trunk/relax --multi='mpi4py'
--log $\sim$/tmp/dispersion/log\_clustered --gui}
+
+When the GUI has started, load the \file{state.bz2} file.
+
For the clustered analysis, we will focus on one group of spins -- those
from residues 59 to 67.
These can be seen to have very similar dynamics:
-\begin{lstlisting}[basicstyle=\scriptsize,numbers=none]
+\begin{lstlisting}[basicstyle=\ttfamily \scriptsize,numbers=none]
# Parameter description: The population for state A.
#
# mol_name res_num res_name spin_num spin_name value
error
@@ -3303,7 +3313,7 @@
[snip]
\end{lstlisting}
-\begin{lstlisting}[basicstyle=\scriptsize,numbers=none]
+\begin{lstlisting}[basicstyle=\ttfamily \scriptsize,numbers=none]
# Parameter description: The exchange rate.
#
# mol_name res_num res_name spin_num spin_name value
error
@@ -3323,7 +3333,7 @@
All other spins will be deselected.
From the non-clustered results, it could be argued that all spins in the
entire system experience the same dynamic process, i.e. have the same $\pA$
and $\kex$ values.
-Such an analysis could be performed at a later stage.
+Such an analysis could be performed at a later stage if desired.
To start the analysis, open the analysis selection wizard as was performed
previously.
Name the analysis as `Dispersion - Hansen (clustered :59 to :67)'.
@@ -3368,5 +3378,123 @@
\end{minipage}
Start the analysis by clicking on the \guibutton{Execute} button.
-
-
+You should notice that the spin cluster printout in the log messages in the
relax controller window now show the text:
+
+\begin{lstlisting}[numbers=none]
+The spin cluster [':59', ':60', ':61', ':62', ':63', ':64', ':65', ':66',
':67'].
+\end{lstlisting}
+
+As residue 60 is deselected, it will not be used in the optimisation or any
part of the analysis.
+The full analysis should take a few hours to complete.
+
+
+% Comparison of the analyses.
+%~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{Dispersion GUI mode -- comparison of the analyses}
+
+To statistically compare the non-clustered and clustered analyses, the
advanced Akaike's Information Criterion (AIC) as derived in
\cite{dAuvergneGooley03} can be used.
+This information is stored within the recorded log files.
+Open the \file{$\sim$/tmp/dispersion/log\_non\_clustered} file and search
for the model selection section.
+The text for residues 59 to 67 should be:
+\begin{lstlisting}[basicstyle=\ttfamily
\tiny,language=relax_log,numbers=none]
+The spin cluster [':59@N'].
+# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 1886.14016 1890.14016
+CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 32.15110 42.15110
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 32.61624 42.61624
+The model from the data pipe 'CR72 - relax_disp (Mon Feb 17 18:00:16 2014)'
has been selected.
+
+
+The spin cluster [':60@N'].
+# Data pipe Num_params_(k)
Num_data_sets_(n) Chi2 Criterion
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2 31
3240.49312 3244.49312
+The model from the data pipe 'No Rex - relax_disp (Mon Feb 17 18:00:16
2014)' has been selected.
+
+
+The spin cluster [':61@N'].
+# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 17285.66217 17289.66217
+CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 95.95234 105.95234
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 92.56628 102.56628
+The model from the data pipe 'NS CPMG 2-site expanded - relax_disp (Mon Feb
17 18:00:16 2014)' has been selected.
+
+
+The spin cluster [':62@N'].
+# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 851.74421 855.74421
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 31.48142 41.48142
+The model from the data pipe 'NS CPMG 2-site expanded - relax_disp (Mon Feb
17 18:00:16 2014)' has been selected.
+
+
+The spin cluster [':63@N'].
+# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 6452.87623 6456.87623
+CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 61.70881 71.70881
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 63.14294 73.14294
+The model from the data pipe 'CR72 - relax_disp (Mon Feb 17 18:00:16 2014)'
has been selected.
+
+
+The spin cluster [':64@N'].
+# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 16028.66123 16032.66123
+CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 29.25973 39.25973
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 30.24274 40.24274
+The model from the data pipe 'CR72 - relax_disp (Mon Feb 17 18:00:16 2014)'
has been selected.
+
+
+The spin cluster [':65@N'].
+# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 2997.14849 3001.14849
+CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 37.54956 47.54956
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 38.74910 48.74910
+The model from the data pipe 'CR72 - relax_disp (Mon Feb 17 18:00:16 2014)'
has been selected.
+
+
+The spin cluster [':66@N'].
+# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 1129.05612 1133.05612
+CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 15.81233 25.81233
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 15.79713 25.79713
+The model from the data pipe 'NS CPMG 2-site expanded - relax_disp (Mon Feb
17 18:00:16 2014)' has been selected.
+
+
+The spin cluster [':67@N'].
+# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 18252.93240 18256.93240
+CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 120.14948 130.14948
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 113.41542 123.41542
+The model from the data pipe 'NS CPMG 2-site expanded - relax_disp (Mon Feb
17 18:00:16 2014)' has been selected.
+\end{lstlisting}
+
+For the log file from the clustered analysis (the
\file{$\sim$/tmp/dispersion/log\_clustered} file), the text should be as
follows:
+\begin{lstlisting}[basicstyle=\ttfamily
\tiny,language=relax_log,numbers=none]
+The spin cluster [':59', ':60', ':61', ':62', ':63', ':64', ':65', ':66',
':67'].
+# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
+No Rex - relax_disp (Sun Feb 23 19:36:51 2014) 16
240 56914.82514 56946.82514
+NS CPMG 2-site expanded - relax_disp (Sun Feb 23 19:36:51 2014) 26
240 510.96553 562.96553
+The model from the data pipe 'NS CPMG 2-site expanded - relax_disp (Sun Feb
23 19:36:51 2014)' has been selected.
+\end{lstlisting}
+
+The numbers for the `NS CPMG 2-site expanded' model can be directly compared.
+This is because the parameter number, data set number, chi-squared value and
AIC value (labelled as `Criterion' in the logs) can be summed for the
non-clustered analysis and then compared to the clustered values.
+
+\begin{center}
+\begin{tabular}{lllll}
+\toprule
+
+Analysis & Parameter & Data set & Chi-squared & AIC value
\\
+ & number (k) & number (n) & value \\
+
+\midrule
+
+Non-clustered & 40 & 248 & 418.011 & 498.011 \\
+Clustered & 26 & 240 & 510.966 & 562.966 \\
+
+\bottomrule
+\end{tabular}
+\end{center}
+
+As the Akaike Information Criterion value is much less for the non-clustered
analysis, then this result is the most parsimonious (the closest to Occam's
razor as defined in frequentist statistics).
+Therefore the non-clustered analysis is a statistically better description
of the experimental data.
+If the assumptions of the same dynamics for all spins (both populations
$\pA$ and exchange rates $\kex$) is correct, the results of the clustered
analysis are nevertheless useful as it can decrease parameter uncertainty.
r22317 - /trunk/docs/latex/dispersion.tex