Author: bugman
Date: Wed Feb 26 13:57:26 2014
New Revision: 22331
URL: http://svn.gna.org/viewcvs/relax?rev=22331&view=rev
Log:
Added spacing in front of all lstlisting environments in the relaxation
dispersion chapter of the manual.
Modified:
trunk/docs/latex/dispersion.tex
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=22331&r1=22330&r2=22331&view=diff
==============================================================================
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Wed Feb 26 13:57:26 2014
@@ -2910,11 +2910,13 @@
There is a shortcut to these previous steps in that the file names and
spectrum IDs can be manually typed into the input elements of the
\uf{spectrum\ufsep{}read\ufus{}intensities} user function wizard page.
For the file names, assuming relax is installed in the base directory
\directory{\ossep{}data\ossep{}relax\ossep{}relax-trunk} and a Unix-like
system is being used, the following text can be added:
+
\begin{lstlisting}[numbers=none]
['/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/reference.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in.bis_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/200.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/266.67.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/333.33.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/400.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/466.67.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/533.33.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/533.33.in.bis_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/600.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/66.667.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/666.67.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/733.33.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/800.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/866.67.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/933.33.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/933.33.in.bis_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/1000.in_sparky']
\end{lstlisting}
The spectrum IDs can be added by copying and pasting the following text,
making sure all text is on one line:
+
\begin{lstlisting}[numbers=none]
['500_reference', '500_133.33', '500_133.33b', '500_200', '500_266.67',
'500_333.33', '500_400', '500_466.67', '500_533.33', '500_533.33b',
'500_600', '500_66.667', '500_666.67', '500_733.33', '500_800', '500_866.67',
'500_933.33', '500_933.33b', '500_1000']
\end{lstlisting}
@@ -2986,6 +2988,7 @@
Change the frequency to 800.0 MHz and continue for the next set of matching
spectrum IDs.
Finally click on \guibutton{Next} to move to the next wizard page.
If you have not used the exact values from the files, the relax controller
window will appear with the warning:
+
\begin{lstlisting}[language=relax_log,numbers=none]
relax> spectrometer.frequency(id='500_reference', frq=500.0, units='MHz')
RelaxWarning: The precise spectrometer frequency should be suppled, a value
such as 500000000 or 5e8 for a 500 MHz machine is not acceptable. Please see
the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in
the Bruker acqus file.
@@ -3151,6 +3154,7 @@
Firstly, to see which models have been chosen for the spin systems and which
have no statistically significant dispersion, find the \file{model.out} file
and double click on it.
You should see the following:
+
\begin{lstlisting}[basicstyle=\ttfamily \scriptsize,numbers=none]
# Parameter description: The dispersion model.
#
@@ -3236,6 +3240,7 @@
To see which spins have been assigned the model `No Rex' due to the
$\Rtwoeff/\Ronerho$ insignificance level of 1.0 rad/s, search the log
messages for `insignificance'.
You should see:
+
\begin{lstlisting}[basicstyle=\ttfamily
\tiny,language=relax_log,numbers=none]
relax> relax_disp.insignificance(level=1.0)
Deselecting spin ':2@N', the maximum dispersion curve difference for all
curves is 0.772528040762 rad/s.
@@ -3273,6 +3278,7 @@
Search for `eliminate' to see which models have been removed due to the
model elimination step (see section~\ref{sect: relaxation dispersion model
elimination} on page~\pageref{sect: relaxation dispersion model elimination}
for details).
For example for the CR72 model:
+
\begin{lstlisting}[basicstyle=\ttfamily
\tiny,language=relax_log,numbers=none]
relax> eliminate(function=None, args=None)
Data pipe 'CR72 - relax_disp (Mon Feb 17 18:00:16 2014)': The pA parameter
of 0.50003 is less than 0.50100, eliminating the spin cluster [':6@N'].
@@ -3358,6 +3364,7 @@
For the clustered analysis, we will focus on one group of spins -- those
from residues :59 to :67.
These can be seen to have very similar dynamics:
+
\begin{lstlisting}[basicstyle=\ttfamily \scriptsize,numbers=none]
# Parameter description: The population for state A.
#
@@ -3447,6 +3454,7 @@
Start the analysis by clicking on the \guibutton{Execute} button.
You should notice that the spin cluster printout in the log messages in the
relax controller window now show the text:
+
\begin{lstlisting}[numbers=none]
The spin cluster [':59', ':60', ':61', ':62', ':63', ':64', ':65', ':66',
':67'].
\end{lstlisting}
@@ -3464,6 +3472,7 @@
This information is stored within the recorded log files.
Open the \file{$\sim$/tmp/dispersion/log\_non\_clustered} file and search
for the model selection section.
The text for residues 59 to 67 should be:
+
\begin{lstlisting}[basicstyle=\ttfamily
\tiny,language=relax_log,numbers=none]
The spin cluster [':59@N'].
# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
@@ -3535,6 +3544,7 @@
\end{lstlisting}
For the log file from the clustered analysis (the
\file{$\sim$/tmp/dispersion/log\_clustered} file), the text should be as
follows:
+
\begin{lstlisting}[basicstyle=\ttfamily
\tiny,language=relax_log,numbers=none]
The spin cluster [':59', ':60', ':61', ':62', ':63', ':64', ':65', ':66',
':67'].
# Data pipe
Num_params_(k) Num_data_sets_(n) Chi2 Criterion
r22331 - /trunk/docs/latex/dispersion.tex