Author: bugman
Date: Wed Sep 19 14:57:03 2012
New Revision: 17507
URL: http://svn.gna.org/viewcvs/relax?rev=17507&view=rev
Log:
Updated the data model chapter of the user manual to cover the handling of
protons.
This change includes the modification of the PDB reading screenshot to
demonstrate the reading of a
specific model and the naming of the molecule.
Modified:
trunk/docs/latex/data_model.tex
trunk/graphics/screenshots/spin_viewer/wizard_read_pdb.eps.gz
trunk/graphics/screenshots/spin_viewer/wizard_read_pdb.png
Modified: trunk/docs/latex/data_model.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/data_model.tex?rev=17507&r1=17506&r2=17507&view=diff
==============================================================================
--- trunk/docs/latex/data_model.tex (original)
+++ trunk/docs/latex/data_model.tex Wed Sep 19 14:57:03 2012
@@ -316,32 +316,33 @@
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/wizard_read_pdb.eps.gz}}
\end{minipage}
-Now select the PDB file you wish to use. The other options in this screen
allow you to handle NMR models and multiple molecules within a single PDB
file. These options are explained in the window. Hovering the mouse over
the options will give additional hints. Now click on \guibutton{Next} to
bring up the spin loading page:
+Now select the PDB file you wish to use. The other options in this screen
allow you to handle NMR models and multiple molecules within a single PDB
file. These options are explained in the window. Hovering the mouse over
the options will give additional hints. In this example, the \nth{3} model
from the 1F3Y PDB file will be read and the single molecule will be named
\guistring{Ap4Aase} to override the default naming of \guistring{1f3y\_mol1}.
Now click on \guibutton{Next} to bring up the spin loading page:
\begin{minipage}[h]{\linewidth}
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/wizard_load_spins_n.eps.gz}}
\end{minipage}
-This is a bit more complicated. In this example we are studying the
backbone dynamics of $^{15}$N spins of a protein. Therefore first set the
spin ID string to \guistring{@N} (which can be selected from the pull down)
and click on \guibutton{Apply} to set up the backbone spins. Do not click on
\guibutton{Next} yet.
+This is a bit more complicated. In this example we are studying the
backbone dynamics of $^{15}$N spins of a protein. Therefore first set the
spin ID string to \guistring{@N} (which can be selected from the pull down)
and click on \guibutton{Apply} to set up the backbone spins. Do not click on
\guibutton{Next} yet. If the current study requires the specification of the
dipole-dipole interaction (for example if it involves relaxation data --
model-free analyses, consistency testing, reduced spectral density mapping;
or the dipolar coupling -- the N-state model or ensemble analyses, the Frame
Order theory) you will also need to load the $^1$H spins as well. Therefore
set the spin ID string to \guistring{@H} and click on \guibutton{Apply} again.
\begin{minipage}[h]{\linewidth}
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/wizard_load_spins_ne1.eps.gz}}
\end{minipage}
-Now change the spin ID string to \guistring{@NE1} and then click on
\guibutton{Next}. This will add spin containers for the tryptophan indole
$^{15}$N spins. Finally click on \guibutton{Finish} to exit the wizard:
+Now change the spin ID string to \guistring{@NE1} and then click on
\guibutton{Next} (or \guibutton{Apply} if the Trp protons \guistring{@HE1}
need to be loaded as well). This will add spin containers for the tryptophan
indole $^{15}$N spins. Finally click on \guibutton{Finish} to exit the
wizard:
\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:
+You should now see something such as:
\begin{minipage}[h]{\linewidth}
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/full.eps.gz}}
\end{minipage}
+If the $^1$H spins have been loaded as well, then you should see exactly
twice as many spin containers as shown above.
% Spins from a sequence file.
@@ -363,7 +364,7 @@
\subsection{Manual construction} \label{sect: GUI - manual construction}
-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
\gui{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.
+Just as in the prompt/script UI mode, the molecules, residues and spins can
be manually added. First add a molecule by right clicking on the \gui{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.
Modified: trunk/graphics/screenshots/spin_viewer/wizard_read_pdb.eps.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/graphics/screenshots/spin_viewer/wizard_read_pdb.eps.gz?rev=17507&r1=17506&r2=17507&view=diff
==============================================================================
Binary files - no diff available.
Modified: trunk/graphics/screenshots/spin_viewer/wizard_read_pdb.png
URL:
http://svn.gna.org/viewcvs/relax/trunk/graphics/screenshots/spin_viewer/wizard_read_pdb.png?rev=17507&r1=17506&r2=17507&view=diff
==============================================================================
Binary files - no diff available.
r17507 - in /trunk: docs/latex/ graphics/screenshots/spin_viewer/