Author: bugman
Date: Tue Feb 25 18:39:33 2014
New Revision: 22318
URL: http://svn.gna.org/viewcvs/relax?rev=22318&view=rev
Log:
Some edits for the tutorial on using the dispersion GUI analysis.
The results of the relax_disp.insignificance user function are now shown to
demonstrate what this
does.
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=22318&r1=22317&r2=22318&view=diff
==============================================================================
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Tue Feb 25 18:39:33 2014
@@ -3140,7 +3140,6 @@
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=\ttfamily \scriptsize,numbers=none]
# Parameter description: The dispersion model.
#
@@ -3224,6 +3223,43 @@
The differences between the `CR72' analytic model and the `NS CPMG 2-site
expanded' numeric model are insignificant.
To see this, open the \file{CR72\ossep{}chi2.agr} and \file{NS CPMG 2-site
expanded\ossep{}chi2.agr} Grace files in the
\directory{$\sim$\ossep{}dispersion\ossep{}log\osus{}non\osus{}clustered}
directory in a text editor and compare the optimised chi-squared values.
+To see which spins have been assigned the model `No Rex' due to the
$\Rtwoeff/\Ronerho$ insignificance level of 1.0 rad/s, search the log
messages for `insignificance'.
+You should see:
+\begin{lstlisting}[basicstyle=\ttfamily
\tiny,language=relax_log,numbers=none]
+relax> relax_disp.insignificance(level=1.0)
+Deselecting spin ':2@N', the maximum dispersion curve difference for all
curves is 0.772528040762 rad/s.
+Deselecting spin ':3@N', the maximum dispersion curve difference for all
curves is 0.572686080104 rad/s.
+Deselecting spin ':4@N', the maximum dispersion curve difference for all
curves is 0.20753288407 rad/s.
+Deselecting spin ':7@N', the maximum dispersion curve difference for all
curves is 0.184120905625 rad/s.
+Deselecting spin ':10@N', the maximum dispersion curve difference for all
curves is 0.746360942576 rad/s.
+Deselecting spin ':11@N', the maximum dispersion curve difference for all
curves is 0.372702361421 rad/s.
+Deselecting spin ':13@N', the maximum dispersion curve difference for all
curves is 0.261522940719 rad/s.
+Deselecting spin ':15@N', the maximum dispersion curve difference for all
curves is 0.743965404051 rad/s.
+Deselecting spin ':16@N', the maximum dispersion curve difference for all
curves is 0.198783344901 rad/s.
+Deselecting spin ':17@N', the maximum dispersion curve difference for all
curves is 0.469568638477 rad/s.
+Deselecting spin ':18@N', the maximum dispersion curve difference for all
curves is 0.720840385548 rad/s.
+Deselecting spin ':19@N', the maximum dispersion curve difference for all
curves is 0.290773963568 rad/s.
+Deselecting spin ':20@N', the maximum dispersion curve difference for all
curves is 0.983669594767 rad/s.
+Deselecting spin ':22@N', the maximum dispersion curve difference for all
curves is 0.507488886605 rad/s.
+Deselecting spin ':24@N', the maximum dispersion curve difference for all
curves is 0.984086643389 rad/s.
+Deselecting spin ':25@N', the maximum dispersion curve difference for all
curves is 0.638104572082 rad/s.
+Deselecting spin ':29@N', the maximum dispersion curve difference for all
curves is 0.525261970487 rad/s.
+Deselecting spin ':33@N', the maximum dispersion curve difference for all
curves is 0.822112754666 rad/s.
+Deselecting spin ':35@N', the maximum dispersion curve difference for all
curves is 0.713976877685 rad/s.
+Deselecting spin ':36@N', the maximum dispersion curve difference for all
curves is 0.413602640091 rad/s.
+Deselecting spin ':37@N', the maximum dispersion curve difference for all
curves is 0.302953864843 rad/s.
+Deselecting spin ':40@N', the maximum dispersion curve difference for all
curves is 0.401535026435 rad/s.
+Deselecting spin ':41@N', the maximum dispersion curve difference for all
curves is 0.805657060225 rad/s.
+Deselecting spin ':43@N', the maximum dispersion curve difference for all
curves is 0.582523964429 rad/s.
+Deselecting spin ':44@N', the maximum dispersion curve difference for all
curves is 0.325638582443 rad/s.
+Deselecting spin ':45@N', the maximum dispersion curve difference for all
curves is 0.947956877688 rad/s.
+Deselecting spin ':49@N', the maximum dispersion curve difference for all
curves is 0.872396631779 rad/s.
+Deselecting spin ':50@N', the maximum dispersion curve difference for all
curves is 0.403543891199 rad/s.
+Deselecting spin ':56@N', the maximum dispersion curve difference for all
curves is 0.468272490195 rad/s.
+Deselecting spin ':57@N', the maximum dispersion curve difference for all
curves is 0.634215047495 rad/s.
+Deselecting spin ':58@N', the maximum dispersion curve difference for all
curves is 0.953109267554 rad/s.
+\end{lstlisting}
+
To see the optimised parameter values, double click on the \file{kex.agr}
file to see the exchange rates.
This will open the \uf{grace\ufsep{}view} user function window by which the
file can be opened.
The default settings produces the following graph:
@@ -3295,7 +3331,6 @@
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=\ttfamily \scriptsize,numbers=none]
# Parameter description: The population for state A.
#
@@ -3379,7 +3414,6 @@
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}
@@ -3496,5 +3530,6 @@
\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.
+Therefore the non-clustered analysis is a statistically better description
of the experimental data for this set of residues.
+For a different spin cluster, this result might be different.
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.
r22318 - /trunk/docs/latex/dispersion.tex