Author: bugman
Date: Mon Sep 3 22:34:03 2012
New Revision: 17441
URL: http://svn.gna.org/viewcvs/relax?rev=17441&view=rev
Log:
Editing of the relaxation curve-fitting and NOE chapters of the user manual.
This is to synchronise the format of the two chapters, and includes the
swapping of text between
them.
Modified:
trunk/docs/latex/curvefit.tex
trunk/docs/latex/noe.tex
Modified: trunk/docs/latex/curvefit.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/curvefit.tex?rev=17441&r1=17440&r2=17441&view=diff
==============================================================================
--- trunk/docs/latex/curvefit.tex (original)
+++ trunk/docs/latex/curvefit.tex Mon Sep 3 22:34:03 2012
@@ -1,7 +1,7 @@
% Relaxation curve-fitting.
%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\chapter[Relaxation curve-fitting]{The $\Rone$ and $\Rtwo$ relaxation rates
-- relaxation curve-fitting}
+\chapter[Relaxation curve-fitting]{The $\Rone$ and $\Rtwo$ relaxation rates
-- relaxation curve-fitting} \label{ch: relax-fit}
\index{relaxation curve-fitting|textbf}
@@ -145,10 +145,15 @@
+% Script UI.
+%%%%%%%%%%%%
+\section{Prompt/script UI mode}
+
+
% The sample script.
-%%%%%%%%%%%%%%%%%%%%
-
-\section{The sample script}
+%~~~~~~~~~~~~~~~~~~~
+
+\subsection{The sample script}
\begin{exampleenv}
\# Script for relaxation curve-fitting. \\
@@ -250,25 +255,44 @@
-% Initialisation of the data pipe and loading of the data.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\section{Initialisation of the data pipe and loading of the data}
-
-The start of this sample script is very similar to that of the NOE
calculation on page~\pageref{NOE initialisation}. The command
-
-\begin{exampleenv}
-pipe.create(`rx', `relax\_fit')
-\end{exampleenv}
-
-initialises the data pipe labelled \promptstring{rx}. The data pipe type is
set to relaxation curve-fitting by the argument \promptstring{relax\_fit}.
The backbone amide nitrogen sequence is extracted from a PDB\index{PDB} file
using the same commands as the NOE calculation script
+% Initialisation of the data pipe.
+%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{Initialisation of the data pipe} \label{Rx initialisation}
+
+The data pipe is simply created by the command
+
+\example{pipe.create(`rx', `relax\_fit')}
+
+This user function will then create a relaxation exponential curve-fitting
specific data pipe labelled \promptstring{rx}. The second argument sets the
pipe type to that of the relaxation curve-fitting. Setting the pipe type is
important so that the program knows which user functions are compatible with
the data pipe, for example in the steady-state NOE analysis the function
\uf{minimise} (see page~\pageref{uf: minimise}) is meaningless as the NOE
values are calculated directly rather than optimised.
+
+
+% Spin systems.
+%~~~~~~~~~~~~~~
+
+\subsection{Setting up the spin systems}
+
+The first thing which need to be completed prior to any spin specific
command is to generate the molecule, residue and spin data structures for
storing the spin specific data. In the sample script above this is generated
from a PDB file, however a plain text file with the sequence information can
be used instead (see the \uf{sequence.read} user function on
page~\pageref{uf: sequence.read} for more details). In the case of the
sample script, the command
\example{structure.read\_pdb(name, `Ap4Aase\_new\_3.pdb')}
\index{PDB}
-\example{structure.load\_spins(spin\_id=`@N')}
-
-To load the peak intensities\index{peak!intensity} into relax the user
function \uf{spectrum.read\_intensities} is executed. Important keyword
arguments to this command are the file name and directory, the spectrum
identification string and the relaxation time period of the experiment in
seconds. By default the file format will be automatically detected.
Currently Sparky\index{software!Sparky}, XEasy\index{software!XEasy},
NMRView\index{software!NMRView}, and generic columnar formatted peak lists
are supported. To be able to import any other type of format please send an
email to the relax development mailing list\index{mailing list!relax-devel}
with the details of the format. Adding support for new formats is trivial.
The following series of commands will load peak intensities from six
different relaxation periods, four of which have been duplicated, from Sparky
peak lists with the peak heights in the 10$^\textrm{th}$ column.
+will load the PDB file \file{Ap4Aase\_new\_3.pdb} into relax. Then
+
+\begin{exampleenv}
+structure.load\_spins(spin\_id=`@N') \\
+structure.load\_spins(spin\_id=`@NE1')
+\end{exampleenv}
+
+will generate the molecule, residue, and spin sequence for the current data
pipe. In this situation there will be a single spin system per residue
generated corresponding to the backbone amide nitrogens as well as $^{15}$N
spins set up for the tryptophan indole nitrogens. Although the 3D
coordinates have been loaded into the program from the PDB file, this
structural information serves no purpose when calculating $\Rone$ and $\Rtwo$
values.
+
+
+% Loading the data.
+%~~~~~~~~~~~~~~~~~~
+
+\subsection{Loading the data}
+
+To load the peak intensities\index{peak!intensity} into relax the user
function \uf{spectrum.read\_intensities} is executed. Important keyword
arguments to this command are the file name and directory, the spectrum
identification string and the relaxation time period of the experiment in
seconds. By default the file format will be automatically detected.
Currently Sparky\index{software!Sparky}, XEasy\index{software!XEasy},
NMRView\index{software!NMRView}, and generic columnar formatted peak lists
are supported. To be able to import any other type of format please send an
email to the relax development mailing list\index{mailing list!relax-devel}
with the details of the format. Adding support for new formats is trivial.
The following series of commands -- an expansion of the \prompt{for} loop in
the sample script -- will load peak intensities from six different relaxation
periods, four of which have been duplicated, from Sparky peak lists with the
peak heights in the 10$^\textrm{th}$ column.
\begin{exampleenv}
spectrum.read\_intensities(file=`T2\_ncyc1.list', spectrum\_id=`1',
relax\_time=0.0176, int\_col=10) \\
Modified: trunk/docs/latex/noe.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/noe.tex?rev=17441&r1=17440&r2=17441&view=diff
==============================================================================
--- trunk/docs/latex/noe.tex (original)
+++ trunk/docs/latex/noe.tex Mon Sep 3 22:34:03 2012
@@ -105,11 +105,11 @@
\subsection{Initialisation of the data pipe} \label{NOE initialisation}
-The data pipe is simply created by the command
+The start of this sample script is very similar to that of the relaxation
curve-fitting calculation on page~\pageref{Rx initialisation}. The command
\example{pipe.create(`NOE', `noe')}
-This user function will then create a NOE calculation specific data pipe
labelled \promptstring{NOE}. The second argument sets the pipe type to that
of the NOE calculation. Setting the pipe type is important so that the
program knows which user functions are compatible with the data pipe, for
example the function \uf{minimise} (see page~\pageref{uf: minimise}) is
meaningless in this sample script as the NOE values are directly calculated
rather than optimised.
+initialises the data pipe labelled \promptstring{NOE}. The data pipe type
is set to the NOE calculation by the argument \promptstring{noe}.
% Spin systems.
@@ -117,19 +117,17 @@
\subsection{Setting up the spin systems}
-The first thing which need to be completed prior to any spin specific
command is to generate the molecule, residue and spin data structures for
storing the spin specific data. In the sample script above this is generated
from a PDB file, however a plain text file with the sequence information can
be used instead (see the \uf{sequence.read} user function on
page~\pageref{uf: sequence.read} for more details). In the case of the
sample script, the command
+The backbone amide nitrogen sequence is extracted from a PDB\index{PDB} file
using the same commands as the relaxation curve-fitting script
(Chapter~\ref{ch: relax-fit}. The command
\example{structure.read\_pdb(`Ap4Aase\_new\_3.pdb')}
\index{PDB}
-will load the PDB file \file{Ap4Aase\_new\_3.pdb} into relax. Then
+will load the PDB file \file{Ap4Aase\_new\_3.pdb} into relax. Then the
following commands will generate both the backbone amide and tryptophan
indole $^{15}$N spins
\begin{exampleenv}
structure.load\_spins(spin\_id=`@N') \\
structure.load\_spins(spin\_id=`@NE1')
\end{exampleenv}
-
-will generate the molecule, residue, and spin sequence for the current data
pipe. In this situation there will be a single spin system per residue
generated corresponding to the backbone amide nitrogens as well as $^{15}$N
spins set up for the tryptophan indole nitrogens. Although the 3D
coordinates have been loaded into the program from the PDB file, this
structural information serves no purpose when calculating NOE values.
% Loading the data.
r17441 - in /trunk/docs/latex: curvefit.tex noe.tex