Author: bugman
Date: Wed Aug 29 12:36:12 2012
New Revision: 17385
URL: http://svn.gna.org/viewcvs/relax?rev=17385&view=rev
Log:
The relax data model chapter of the user manual now uses the higher quality
graphics.
Modified:
trunk/docs/latex/data_model.tex
Modified: trunk/docs/latex/data_model.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/data_model.tex?rev=17385&r1=17384&r2=17385&view=diff
==============================================================================
--- trunk/docs/latex/data_model.tex (original)
+++ trunk/docs/latex/data_model.tex Wed Aug 29 12:36:12 2012
@@ -27,7 +27,7 @@
\subsection{Data pipes}
\begin{figure*}[h]
-\includegraphics[width=2cm, bb=0 0 567 567]{graphics/wizards/pipe.eps.gz}
+\includegraphics[width=3cm, bb=0 0 1701
1701]{graphics/misc/pipe_600x600.eps.gz}
\end{figure*}
The first thing one must do when relax is launched is to create a data pipe.
When using the GUI, a base data pipe will be created when opening one of the
automatic analyses via the analysis selection window (see figure~\ref{fig:
screenshot: analysis wizard} on page~\pageref{fig: screenshot: analysis
wizard}). This will also create a data pipe bundle for the analysis
(\textit{vide infra}). Alternatively the data pipe editor window can be used
to create data pipes (see figure~\ref{fig: screenshot: pipe editor} on
page~\pageref{fig: screenshot: pipe editor}). For the prompt/scripting
modes, or the \texttt{`User functions $\to$ pipe $\to$ create'} menu entry, a
data pipe can be initialised by specifying the unique name of the data pipe
and the data pipe type:
@@ -46,7 +46,7 @@
\subsection{Data pipe bundles}
\begin{figure*}[h]
-\includegraphics[width=2cm, bb=14 14 175
175]{graphics/wizards/pipe_bundle.eps.gz}
+\includegraphics[width=3cm, bb=0 0 1701
1701]{graphics/misc/pipe_bundle_600x600.eps.gz}
\end{figure*}
Related data pipes can be grouped into a `bundle'. For example if the data
pipes \texttt{`sphere'}, \texttt{`oblate spheroid'}, \texttt{`prolate
spheroid'}, and \texttt{`ellipsoid'} preexist, these can be grouped into a
bundle called \texttt{`diffusion tensors'} with the following series of user
function calls:
@@ -78,7 +78,7 @@
\subsection{Molecule containers}
\begin{figure*}[h]
-\includegraphics[width=2cm, bb=0 0 567 567]{graphics/wizards/molecule.eps.gz}
+\includegraphics[width=3cm, bb=0 0 1701
1701]{graphics/misc/molecule_600x600.eps.gz}
\end{figure*}
The spin containers are part of a nested set of containers, and are
graphically depicted in the spin viewer window of the GUI in figure~\ref{fig:
screenshot: spin viewer} on page~\pageref{fig: screenshot: spin viewer}. As
can be seen from the figure, the top level holds a single molecular
container. Multiple molecular containers can be present if the study is of a
molecular complex. Using the GUI menus or the prompt/scripting mode,
molecule containers can be manually created with the user function:
@@ -95,7 +95,7 @@
\subsection{Residue containers}
\begin{figure*}[h]
-\includegraphics[width=2cm, bb=0 0 567 567]{graphics/wizards/residue.eps.gz}
+\includegraphics[width=3cm, bb=0 0 1701
1701]{graphics/misc/residue_600x600.eps.gz}
\end{figure*}
Nested within the molecule containers are residue containers. These are
graphically depicted in the spin viewer window (see figure~\ref{fig:
screenshot: spin viewer} on page~\pageref{fig: screenshot: spin viewer}).
Each molecule container can possess multiple residues. These require either
a unique residue number or unique residue name. For organic molecules where
the residue concept is meaningless, all spin containers can be held within a
single unnamed and unnumbered residue container. Using the GUI menus or the
prompt/scripting mode, residue containers can be manually created with the
user function:
@@ -109,10 +109,11 @@
% Spin containers.
%~~~~~~~~~~~~~~~~~
+\newpage
\subsection{Spin containers}
\begin{figure*}[h]
-\includegraphics[width=2cm, bb=0 0 567 567]{graphics/wizards/spin.eps.gz}
+\includegraphics[width=3cm, bb=0 0 1701
1701]{graphics/misc/spin_600x600.eps.gz}
\end{figure*}
Spin containers are nested within a residue container (again graphically
depicted in the spin viewer window in figure~\ref{fig: screenshot: spin
viewer} on page~\pageref{fig: screenshot: spin viewer}). Multiple spin
containers can exist per residue. This allows, for example, a single
model-free analysis simultaneously on the backbone nitrogen spins, side-chain
tryptophan indole nitrogen spins and alpha carbon spins. Or, for example,
studying the pseudocontact shifts for all nitrogen, carbon and proton spins
in the molecule simultaneously.
@@ -153,7 +154,7 @@
\section{Interatomic data containers}
\begin{figure*}[h]
-\includegraphics[width=3cm, bb=14 14 95
148]{graphics/wizards/dipole_pair/NH_dipole_pair.eps.gz}
+\includegraphics[width=3cm, bb=0 0 1701
1701]{graphics/wizards/dipole_pair/NH_dipole_pair_600x600.eps.gz}
\end{figure*}
Separate from the spin containers, yet strongly linked to them, are the
interatomic data containers. These containers are grouped together within
the same data pipe as the spins they point to. These define interactions
between two spins located anywhere within the molecule, residue and spin
nested data structure. These are automatically created when reading in data
defined between two spins such as RDCs and NOE distance constraints. They
can also be created using the \texttt{`dipole\_pair.define'} user function:
@@ -169,7 +170,7 @@
\section{Structural data}
\begin{figure*}[h]
-\includegraphics[width=3cm, bb=14 14 215
293]{graphics/wizards/n_state_model.eps.gz}
+\includegraphics[width=3cm, bb=0 0 1701
1701]{graphics/misc/n_state_model/phthalic_acid_ens_600x600.eps.gz}
\end{figure*}
3D structural data is stored at the level of the current data pipe. This
data is completely separate from the molecule, residue and spin data
structure. However the structural data can be used to generate the spin
containers. For example, assuming a data pipe is already present:
@@ -199,7 +200,7 @@
\section{Sequence file}
\begin{figure*}[h]
-\includegraphics[width=2cm, bb=0 0 567 567]{graphics/wizards/sequence.eps.gz}
+\includegraphics[width=3cm, bb=0 0 1701
1701]{graphics/misc/sequence_600x600.eps.gz}
\end{figure*}
Alternatively to setting up the molecule, residue, and spin containers via
3D structural data, a plain text columnar formatted file can be used. This
is useful for when no 3D structure exists for the molecule. For example:
r17385 - /trunk/docs/latex/data_model.tex