Author: bugman
Date: Mon Sep 3 11:43:36 2012
New Revision: 17427
URL: http://svn.gna.org/viewcvs/relax?rev=17427&view=rev
Log:
More rearrangements of data model and NOE chapters of the relax manual.
The GUI spin deselection part of the NOE chapter has been shifted into the
data model chapter. And
the GUI loading of spins from a sequence file section has been completed.
Modified:
trunk/docs/latex/data_model.tex
trunk/docs/latex/noe.tex
Modified: trunk/docs/latex/data_model.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/data_model.tex?rev=17427&r1=17426&r2=17427&view=diff
==============================================================================
--- trunk/docs/latex/data_model.tex (original)
+++ trunk/docs/latex/data_model.tex Mon Sep 3 11:43:36 2012
@@ -286,12 +286,14 @@
\begin{minipage}[h]{\linewidth}
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/blank.eps.gz}}
+\label{figure: spin viewer blank}
\end{minipage}
At this point, click on the `Load spins' button (or the `Load spins' menu
entry from the right click pop up menu) to launch the spin loading wizard. A
number of options will be presented to you:
\begin{minipage}[h]{\linewidth}
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/wizard_start.eps.gz}}
+\label{figure: spin viewer wizard start}
\end{minipage}
As in the sample script, here the spins will be loaded from a PDB file. The
next series of screenshots will only demonstrate this option. If you do not
have a 3D structure file, then you will need to load the sequence data from a
special text file. See the \texttt{sequence.read} user function on
page~\pageref{uf: sequence.read} for more details. The wizard will present
this user function to you if you choose `From a file containing sequence
data'. After selecting `From a new PDB structure file' and clicking on next,
you will see:
@@ -317,6 +319,7 @@
\begin{minipage}[h]{\linewidth}
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/wizard_end.eps.gz}}
+\label{figure: spin viewer end}
\end{minipage}
You should now see something like:
@@ -325,7 +328,6 @@
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/full.eps.gz}}
\end{minipage}
-The spin viewer window can now be closed.
% Sequence file.
@@ -333,6 +335,14 @@
\subsection{Sequence file} \label{sect: GUI - sequence file}
+Starting from the empty spin viewer window on page~\pageref{figure: spin
viewer blank}), click on the `Load spins' button. You will then see the spin
loading wizard (see page~\pageref{figure: spin viewer wizard start}). Select
the option for reading data from a sequence file. You should then see:
+
+\begin{minipage}[h]{\linewidth}
+\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/wizard_sequence.eps.gz}}
+\end{minipage}
+
+Change the `Free format file settings' as needed. Click on `Next' to reach
the wizard ending page (see~\pageref{figure: spin viewer end}). Finally
click on `Finish' to exit the wizard.
+
% Manual construction.
%~~~~~~~~~~~~~~~~~~~~~
@@ -342,6 +352,30 @@
Just like in the prompt/script UI mode, the molecules, residues and spins
can be manually added. First add a molecule by right clicking on the `Spin
system information' element and selecting the relevant entry in the popup
menu. Then right click on the newly created molecule container to add
residues, and right click on residue containers to add spins.
+% Deselect spins.
+%~~~~~~~~~~~~~~~~
+
+\subsection{Deselect spins} \label{sect: GUI - deselect spins}
+
+To deselect spins (for example if they are unresolved, overlapping peaks),
click on the `User functions$\to$deselect$\to$read' menu item from the main
relax window or the spin viewer window:
+
+\begin{minipage}[h]{\linewidth}
+\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/noe_analysis/analysis_tab3.eps.gz}}
+\end{minipage}
+
+Select the file listing the unresolved spins and change the column numbers
in the `Free format file settings' GUI element as needed:
+
+\begin{minipage}[h]{\linewidth}
+\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/noe_analysis/deselect.eps.gz}}
+\end{minipage}
+
+Alternatively the spin editor window can be reopened and the spins manually
deselected by right clicking on them and selecting `Deselect'. Returning to
the spin editor window, you should now see certain spins coloured grey:
+
+\begin{minipage}[h]{\linewidth}
+\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/deselect.eps.gz}}
+\end{minipage}
+
+
% The next steps.
%%%%%%%%%%%%%%%%%
Modified: trunk/docs/latex/noe.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/noe.tex?rev=17427&r1=17426&r2=17427&view=diff
==============================================================================
--- trunk/docs/latex/noe.tex (original)
+++ trunk/docs/latex/noe.tex Mon Sep 3 11:43:36 2012
@@ -337,7 +337,15 @@
\subsection{Setting up the spin systems}
-Just as in the prompt and scripting UI modes, the molecule, residue and spin
data structures need to be set up prior to the loading of any spin specific
data. The `Spin systems' GUI element is used for this purpose. Before any
spin systems have been set up, this should say something like `0 spins loaded
and selected'. To fix this, click on the `Spin editor' button and you should
then see the spin viewer window. The next steps are fully described in
section~\ref{sect: GUI - structural data} on page~\pageref{sect: GUI -
structural data} for PDB files or section~\ref{sect: GUI - structural data}
on page~\pageref{sect: GUI - structural data} for a sequence file.
+Just as in the prompt and scripting UI modes, the molecule, residue and spin
data structures need to be set up prior to the loading of any spin specific
data. The `Spin systems' GUI element is used for this purpose. Before any
spin systems have been set up, this should say something like `0 spins loaded
and selected'. To fix this, click on the `Spin editor' button and you should
then see the spin viewer window. The next steps are fully described in
section~\ref{sect: GUI - structural data} on page~\pageref{sect: GUI -
structural data} for PDB files or section~\ref{sect: GUI - structural data}
on page~\pageref{sect: GUI - structural data} for a sequence file. The spin
viewer window can now be closed.
+
+
+% Unresolved spins.
+%~~~~~~~~~~~~~~~~~~
+
+\subsection{Unresolved spins}
+
+Using the unresolved spins file as described in the prompt/script UI
sections, the same spins can be deselected at this point. See
Section~\ref{sect: GUI - deselect spins} on page~\pageref{sect: GUI -
deselect spins} for the details of how to deselect the spins in the GUI.
% Loading the data.
@@ -398,30 +406,6 @@
\end{minipage}
-% Unresolved spins.
-%~~~~~~~~~~~~~~~~~~
-
-\subsection{Unresolved spins}
-
-Using the unresolved spins file as described in the prompt/script UI
sections, the same spins will be deselected here. Click on the `User
functions$\to$deselect$\to$read' menu item:
-
-\begin{minipage}[h]{\linewidth}
-\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/noe_analysis/analysis_tab3.eps.gz}}
-\end{minipage}
-
-Select the `unresolved' file and change the column numbers in the `Free
format file settings' GUI element as follows:
-
-\begin{minipage}[h]{\linewidth}
-\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/noe_analysis/deselect.eps.gz}}
-\end{minipage}
-
-Alternatively the spin editor window can be reopened and the spins manually
deselected by right clicking on them and selecting `Deselect'. Returning to
the spin editor window, you should now see certain spins coloured grey:
-
-\begin{minipage}[h]{\linewidth}
-\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/noe_analysis/spin_viewer_deselect.eps.gz}}
-\end{minipage}
-
-
% The NOE.
%~~~~~~~~~
r17427 - in /trunk/docs/latex: data_model.tex noe.tex