Author: bugman
Date: Thu Sep 6 11:19:43 2012
New Revision: 17469
URL: http://svn.gna.org/viewcvs/relax?rev=17469&view=rev
Log:
Editing and a number of fixes/cleanups for the consistency testing chapter of
the user manual.
Modified:
trunk/docs/latex/consistency_tests.tex
Modified: trunk/docs/latex/consistency_tests.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/consistency_tests.tex?rev=17469&r1=17468&r2=17469&view=diff
==============================================================================
--- trunk/docs/latex/consistency_tests.tex (original)
+++ trunk/docs/latex/consistency_tests.tex Thu Sep 6 11:19:43 2012
@@ -24,7 +24,7 @@
\item[$F_{R_2}$] A consistency function proposed by \citet{Fushman98}.
\end{description}
-Different methods exist to compare tests values calculated from one field to
another. These include correlation plots and histograms, and calculation of
correlation, skewness and kurtosis coefficients. The details of how to
interpret such analyses are avaliable at the end of this section in Section
\ref{sec: Visualisation and data output}.
+Different methods exist to compare tests values calculated from one field to
another. These include correlation plots and histograms, and calculation of
correlation, skewness and kurtosis coefficients. The details of how to
interpret such analyses are avaliable at the end of this chapter in
Section~\ref{sec: Visualisation and data output}.
For more details on the implementation within relax, see:
@@ -43,19 +43,21 @@
\begin{itemize}
\item \bibentry{Morin11}
\end{itemize}
+
% Script UI.
%%%%%%%%%%%%
+
\section{Prompt/script UI mode}
-The consistency testing analysis is only available via the prompt/script UI
modes -- no GUI auto-analysis has yet been built.
+The consistency testing analysis is only available via the prompt/script UI
modes -- no GUI auto-analysis has yet been built by a relax power-user.
% The sample script.
%~~~~~~~~~~~~~~~~~~~
-\subsection{The sample script}
+\subsection{The sample script} \label{sect: consistency tests - sample
script}
The following script can be found in the \directory{sample\_scripts}
directory.
@@ -72,7 +74,7 @@
\\
The description of the consistency testing approach: \\
\\
- \citet{MorinGagne09a} \\
+ Morin \& Gagne (2009a) Simple tests for the validation of multiple field
spin relaxation data. J. Biomol. NMR, 45: 361-372.
http://dx.doi.org/10.1007/s10858-009-9381-4 \\
\\
The origins of the equations used in the approach: \\
\\
@@ -186,7 +188,7 @@
\section{Relaxation data loading}
-The loading of relaxation data is straight forward. This is performed prior
to the creation of the proton spins so that the data is loaded only into the
$^{15}$N spin containers and not both spins for each residue. Only data for
a single field strength can be loaded:
+The loading of relaxation data is straight forward. This is performed prior
to the creation of the proton spins so that the data is loaded only into the
$^{15}$N spin containers and not both spins for each spin system. Note that
if the relaxation data files contain spin information, then this order is not
important. For this analysis, only data for a single field strength can be
loaded:
\begin{exampleenv}
relax\_data.read(ri\_id=`R1\_600', ri\_type=`R1', frq=600.0*1e6,
file=`r1.600.out', res\_num\_col=1, data\_col=3, error\_col=4) \\
@@ -220,7 +222,7 @@
value.set(val=-172 * 1e-6, param=`csa')
\end{exampleenv}
-For the angle between the 15N-1H vector and the principal axis of the 15N
chemical shift tensor, the user function call is:
+For the angle in degrees between the $^{15}$N-$^1$H vector and the principal
axis of the $^{15}$N chemical shift tensor, the user function call is:
\begin{exampleenv}
value.set(val=15.7, param=`orientation')
@@ -269,17 +271,14 @@
\item See if the correlation plot is centered around a perfect correlation
or skewed away (approach A), or if the values are centered around 1 in the
histogram (approach B). If yes, data from multiple magnetic fields is
consistent from one magnetic field to another. If no, data is inconsistent.
In the case where inconsistency arises, if data from more than two magnetic
fields is avaliable, more than one pair of data can be checked and the
inconsistent magnetic field data can be identified.
\end{itemize}
-An example of such an analysis is shown in Figure \ref{fig: consistency
analysis} below
-
\begin{figure*}[h]
\label{fig: consistency analysis}
\centerline{\includegraphics[width=0.9\textwidth, bb=5 2 1244
669]{graphics/analyses/consistency_testing/consistency__J0_PSE-4.eps.gz}}
-\caption[Example of consistency testing visual analysis]{Example of
consistency testing visual analysis. Relaxation data from three different
magnetic fields are compared. For each pair of magnetic field, a correlation
plot of the calculated $J(0)$ values (approach A, top) as well as an
histogram of the ration of calculated $J(0)$ values (approach B, bottom) are
shown. Data from \citep{MorinGagne09b} is used for the purpose of this
example.}
+\caption[Example of consistency testing visual analysis]{Example of
consistency testing visual analysis. Relaxation data from three different
magnetic fields are compared. For each pair of magnetic field, a correlation
plot of the calculated $J(0)$ values (approach A, top) as well as an
histogram of the ration of calculated $J(0)$ values (approach B, bottom) are
shown. These graphs must be manually created from the output of the sample
script shown in section~\ref{sect: consistency tests - sample script}. Data
from \citep{MorinGagne09b} is used for the purpose of this example.}
\end{figure*}
-As shown in Figure \ref{fig: consistency analysis}, the example data
displays both consistent and inconsistent data. In fact, data recorded at 500
MHz and 600 MHz are consistent together, whereas data recorded at 800 MHz is
not consistent with data recorded at 500 MHz nor 600 MHz. Since more than
two magnetic fields were used, this allowed the identification of the data
from 800 MHz as the inconsistent data, as data from 500 MHz is consistent
with data from 600 MHz, and vice-versa. In this particular example, this
allowed the authors to take special care with data at 800 MHz.
-
-This inconsistency of 800 MHz data is seen on the correlation plot (toop) by
a deviation from the dotted line (which represents the theoretical situation
when equal $J(0)$ values are extracted from both magnetic fields. It is also
observable in the histogram (bottom) where the ration of the data from two
magnetic fields is not centered around 0. In fact, there seems to be a
systematic shift of the calculated $J(0)$ values at 800 MHz when compared to
the two other magnetic fields. This is caused by a similar shift in the
experimental $R_2$ (transversal relaxation rate) data.
-
-For the 500 MHz and 600 MHz data pair, the data are centered around the
dotted line in the correlation plot (approach A, top left) as well as
centered around a value of 1 in the histogram comparing the ratios of values
from both magnetic fields (approach B, bottom left). Of course, there are
some outsider values even in the case of consistent data. There are caused by
specific dynamic characteristics of these spins and are different from
systematic inconsistencies such as depicted in the example above with the
data recorded at 800 MHz.
-
+An example of such an analysis is shown in Figure~\ref{fig: consistency
analysis}. This example displays both consistent and inconsistent data. As
the figure shows, the data recorded at 500 MHz and 600 MHz are consistent
with each other whereas the data recorded at 800 MHz is consistent with the
neither the 500 MHz nor 600 MHz data. Since more than two magnetic fields
were used, this allowed the identification of the 800 MHz data as being
inconsistent allowing the authors to take special care with this data set.
+
+The 800 MHz data inconsistency is seen in the correlation plots (top) by a
deviation from the dotted line (which represents the theoretical situation
when equal $J(0)$ values are extracted from both magnetic fields. It is also
observable in the histograms (bottom) where the ratio of the data from two
magnetic fields is not centered at 1.0. In fact, there seems to be a
systematic shift of the calculated $J(0)$ values at 800 MHz when compared to
the two other magnetic fields. This is caused by a similar shift in the
experimental $\Rtwo$ (transversal relaxation rate) data.
+
+For the 500 MHz and 600 MHz data pair, the data are centered around the
dotted line in the correlation plot (approach A, top left) as well as
centered around a value of 1.0 in the histogram comparing the ratios of
values from both magnetic fields (approach B, bottom left). Of course, there
are some outlier values even in the case of consistent data. There are
caused by specific dynamic characteristics of these spins and are different
from systematic inconsistencies such as depicted in the example above with
the data recorded at 800 MHz.
r17469 - /trunk/docs/latex/consistency_tests.tex