Author: bugman
Date: Wed Mar 26 18:42:57 2014
New Revision: 22546
URL: http://svn.gna.org/viewcvs/relax?rev=22546&view=rev
Log:
Fix for the line numbering for the NOE analysis sample script in the user
manual.
The line numbering for the code snippets did not match that of the full
sample script shown at the
start of that section of the NOE chapter.
Modified:
trunk/docs/latex/noe.tex
Modified: trunk/docs/latex/noe.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/noe.tex?rev=22546&r1=22545&r2=22546&view=diff
==============================================================================
--- trunk/docs/latex/noe.tex (original)
+++ trunk/docs/latex/noe.tex Wed Mar 26 18:42:57 2014
@@ -192,7 +192,7 @@
For the reference spectrum the RMSD was approximately 3600 whereas in the
saturated spectrum the RMSD was 3000.
These errors are set by the commands
-\begin{lstlisting}[firstnumber=21]
+\begin{lstlisting}[firstnumber=19]
# Set the errors.
spectrum.baseplane_rmsd(error=3600, spectrum_id='ref_ave')
spectrum.baseplane_rmsd(error=3000, spectrum_id='sat_ave')
@@ -201,7 +201,7 @@
For the residue G114, the noise levels are significantly increased compared
to the rest of the protein as the peak is located close to the water signal.
The higher errors for this residue are specified by the commands
-\begin{lstlisting}[firstnumber=25]
+\begin{lstlisting}[firstnumber=23]
# Individual residue errors.
spectrum.baseplane_rmsd(error=122000, spectrum_type='ref', res_num=114)
spectrum.baseplane_rmsd(error=8500, spectrum_type='sat', res_num=114)
@@ -211,7 +211,7 @@
See the documentation for the \uf{spectrum\ufsep{}error\ufus{}analysis} user
function on page~\pageref{uf: spectrum.error_analysis} for all possible
options.
This user function needs to be executed at this stage to correctly set up
the errors for all spin systems:
-\begin{lstlisting}[firstnumber=29]
+\begin{lstlisting}[firstnumber=27]
# Peak intensity error analysis.
spectrum.error_analysis()
\end{lstlisting}
@@ -225,7 +225,7 @@
As the peaks of certain spins overlap to such an extent that the heights or
volumes cannot be resolved, a simple text file was created called
\promptstring{unresolved} in which each line consists of the residue number
followed by the atom name.
By using the command
-\begin{lstlisting}[firstnumber=32]
+\begin{lstlisting}[firstnumber=30]
# Deselect unresolved spins.
deselect.read(name, file='unresolved', res_num_col=1, spin_name_col=2)
\end{lstlisting}
@@ -242,7 +242,7 @@
At this point the NOE can be calculated.
The user function
-\begin{lstlisting}[firstnumber=35]
+\begin{lstlisting}[firstnumber=33]
# Calculate the NOEs.
calc()
\end{lstlisting}
@@ -262,7 +262,7 @@
\noindent where $\sigma_{sat}$ and $\sigma_{ref}$ are the peak intensity
errors in the saturated and reference spectra respectively.
To create a file of the NOEs the command
-\begin{lstlisting}[firstnumber=38]
+\begin{lstlisting}[firstnumber=36]
# Save the NOEs.
value.write(param='noe', file='noe.out', force=True)
\end{lstlisting}
@@ -317,7 +317,7 @@
The highly flexible relax user function \uf{grace\ufsep{}write} is capable
of producing 2D plots of any x-y data sets.
The two commands
-\begin{lstlisting}[firstnumber=41]
+\begin{lstlisting}[firstnumber=39]
# Create Grace files.
grace.write(y_data_type='intensities', file='intensities.agr', force=True)
grace.write(y_data_type='noe', file='noe.agr', force=True)
@@ -329,7 +329,7 @@
These can be visualised by opening the file within Grace.
However relax will do that for you with the commands
-\begin{lstlisting}[firstnumber=45]
+\begin{lstlisting}[firstnumber=43]
# View the Grace files.
grace.view(file='intensities.agr')
grace.view(file='noe.agr')
r22546 - /trunk/docs/latex/noe.tex