Author: semor
Date: Wed Sep 5 14:16:17 2012
New Revision: 17453
URL: http://svn.gna.org/viewcvs/relax?rev=17453&view=rev
Log:
Added text to detail the usage of the consistency testing script.
This text was modified from the corresponding text for jw_mapping.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id:
<CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@xxxxxxxxxxxxxx>)
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=17453&r1=17452&r2=17453&view=diff
==============================================================================
--- trunk/docs/latex/consistency_tests.tex (original)
+++ trunk/docs/latex/consistency_tests.tex Wed Sep 5 14:16:17 2012
@@ -116,7 +116,7 @@
value.set(val=-172 * 1e-6, param=`csa') \\
\\
\# Set the angle between the 15N-1H vector and the principal axis of the 15N
chemical shift tensor \\
-value.set(val=15.7, param=`orientation')
+value.set(val=15.7, param=`orientation')
\\
\# Set the approximate correlation time. \\
value.set(val=13 * 1e-9, param=`tc') \\
@@ -148,4 +148,114 @@
state.save(`save', force=True)
\end{exampleenv}
-This is similar in spirit to the reduced spectral density mapping sample
script, so please see Chapter~\ref{ch: J(w) mapping} on page~\pageref{ch:
J(w) mapping} if you require a detailed description of the usage of this
script.
+This is similar in spirit to the reduced spectral density mapping sample
script (Chapter~\ref{ch: J(w) mapping} on page~\pageref{ch: J(w) mapping}).
+
+
+% Data pipe and spin system setup.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{Data pipe and spin system setup}
+
+The steps for setting up relax and the data model concept are described in
full detail in Chapter~\ref{ch: data model}. The first step, as for all
analyses in relax, is to create a data pipe for storing all the data:
+
+\begin{exampleenv}
+pipe.create(pipe\_name=`my\_protein', pipe\_type=`ct')
+\end{exampleenv}
+
+Then, in this example, the $^{15}$N spins are created from one of the NOE
relaxation data files (Chapter~\ref{ch: NOE}):
+
+\begin{exampleenv}
+sequence.read(file=`noe.600.out', res\_num\_col=1, res\_name\_col=2) \\
+spin.name(name=`N') \\
+spin.element(element=`N') \\
+spin.isotope(isotope=`15N', spin\_id=`@N')
+\end{exampleenv}
+
+Skipping the relaxation data loading, the next part of the analysis is to
create protons attached to the nitrogens for the magnetic dipole-dipole
relaxation interaction:
+
+\begin{exampleenv}
+sequence.attach\_protons()
+\end{exampleenv}
+
+This is needed to define the magnetic dipole-dipole interaction which
governs relaxation.
+
+
+
+% Relaxation data loading.
+%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\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:
+
+\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) \\
+relax\_data.read(ri\_id=`R2\_600', ri\_type=`R2', frq=600.0*1e6,
file=`r2.600.out', res\_num\_col=1, data\_col=3, error\_col=4) \\
+relax\_data.read(ri\_id=`NOE\_600', ri\_type=`NOE', frq=600.0*1e6,
file=`noe.600.out', res\_num\_col=1, data\_col=3, error\_col=4)
+\end{exampleenv}
+
+The frequency of the data must also be explicitly specified:
+
+\begin{exampleenv}
+consistency\_tests.set\_frq(frq=600.0 * 1e6) \\
+\end{exampleenv}
+
+
+
+% Relaxation interactions.
+%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{Relaxation interactions}
+
+Prior to calculating the $J(0)$, $F_\eta$, and $F_{R_2}$ values, the
physical interactions which govern relaxation of the spins must be defined.
For the magnetic dipole-dipole relaxation interaction, the user functions are:
+
+\begin{exampleenv}
+dipole\_pair.define(spin\_id1=`@N', spin\_id2=`@H', direct\_bond=True) \\
+dipole\_pair.set\_dist(spin\_id1=`@N', spin\_id2=`@H', ave\_dist=1.02 *
1e-10)
+\end{exampleenv}
+
+For the chemical shift relaxation interaction, the user function call is:
+
+\begin{exampleenv}
+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:
+
+\begin{exampleenv}
+value.set(val=15.7, param=`orientation')
+\end{exampleenv}
+
+
+% Calculation and error propagation.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{Calculation and error propagation}
+
+Optimisation for this analysis is not needed as this is a direct
calculation. Therefore the $J(0)$, $F_\eta$, and $F_{R_2}$ values are simply
calculated with the call:
+
+\begin{exampleenv}
+calc()
+\end{exampleenv}
+
+The propagation of errors is more complicated. The Monte Carlo simulation
framework of relax can be used to propagate the relaxation data errors to the
spectral density errors. As this is a direct calculation, this collapses
into the standard bootstrapping method. The normal Monte Carlo user
functions can be called:
+
+\begin{exampleenv}
+monte\_carlo.setup(number=500) \\
+monte\_carlo.create\_data() \\
+calc() \\
+monte\_carlo.error\_analysis()
+\end{exampleenv}
+
+In this case, the \uf{monte\_carlo.initial\_values} user function call is
not required.
+
+
+% Visualisation and data output.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{Visualisation and data output}
+
+The rest of the script is used to output the results to 2D Grace files for
visualisation (the \uf{grace.view} user function calls will launch Grace with
the created files), and the output of the values into plain text files.
+
+However, simply visualizing the calculated $J(0)$, $F_\eta$, and $F_{R_2}$
values this way does not allow proper consistency testing. Indeed, for
assessing the consistency of relaxation data using these tests, different
methods exist to compare values calculated from one field to another. These
include correlation plots and histograms, and calculation of correlation,
skewness and kurtosis coefficients.
+
r17453 - /trunk/docs/latex/consistency_tests.tex