Hi Seb, I have just performed a little clean up of the "Consistency testing" chapter of the relax manual. This is now in a pretty good shape to ship out to users. I was wondering if you'd like to add some small text as the end, a last paragraph maybe, explaining why the script generates the F_eta and F_R2 values. From reading the references, this is obvious. But if a user reads this chapter as it is before jumping to your papers, they will be confused.
Cheers, Edward On 6 September 2012 11:19, <[email protected]> wrote: > 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. > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
