Author: bugman
Date: Thu Jun 20 00:10:12 2013
New Revision: 20222
URL: http://svn.gna.org/viewcvs/relax?rev=20222&view=rev
Log:
Improvements to the script UI section of the NOE chapter of the user manual.
The lstlisting environments now have the correct numbering to match the
script at the start,
comments have been copied into the split up script elements, and a few
comments improved.
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=20222&r1=20221&r2=20222&view=diff
==============================================================================
--- trunk/docs/latex/noe.tex (original)
+++ trunk/docs/latex/noe.tex Thu Jun 20 00:10:12 2013
@@ -73,7 +73,7 @@
# Peak intensity error analysis.
spectrum.error_analysis()
-# Deselect unresolved residues.
+# Deselect unresolved spins.
deselect.read(file='unresolved', res_num_col=1, spin_name_col=2)
# Calculate the NOEs.
@@ -82,12 +82,12 @@
# Save the NOEs.
value.write(param='noe', file='noe.out', force=True)
-# Create grace files.
+# Create Grace files.
grace.write(y_data_type='ref', file='ref.agr', force=True)
grace.write(y_data_type='sat', file='sat.agr', force=True)
grace.write(y_data_type='noe', file='noe.agr', force=True)
-# View the grace files.
+# View the Grace files.
grace.view(file='ref.agr')
grace.view(file='sat.agr')
grace.view(file='noe.agr')
@@ -108,7 +108,8 @@
The start of this sample script is very similar to that of the relaxation
curve-fitting calculation on page~\pageref{Rx initialisation}. The command
-\begin{lstlisting}
+\begin{lstlisting}[firstnumber=3]
+# Create the data pipe.
pipe.create('NOE', 'noe')
\end{lstlisting}
@@ -122,14 +123,15 @@
The backbone amide nitrogen sequence is extracted from a PDB\index{PDB} file
using the same commands as the relaxation curve-fitting script
(Chapter~\ref{ch: relax-fit}. The command
-\begin{lstlisting}
+\begin{lstlisting}[firstnumber=6]
+# Load the sequence from a PDB file.
structure.read_pdb('Ap4Aase_new_3.pdb')
\end{lstlisting}
\index{PDB}
will load the PDB file \file{Ap4Aase\_new\_3.pdb} into relax. Then the
following commands will generate both the backbone amide and tryptophan
indole $^{15}$N spins
-\begin{lstlisting}
+\begin{lstlisting}[firstnumber=8]
structure.load_spins(spin_id='@N')
structure.load_spins(spin_id='@NE1')
\end{lstlisting}
@@ -142,7 +144,8 @@
The commands
-\begin{lstlisting}
+\begin{lstlisting}[firstnumber=11]
+# Load the reference spectrum and saturated spectrum peak intensities.
spectrum.read_intensities(file='ref.list', spectrum_id='ref_ave',
heteronuc='N', proton='HN')
spectrum.read_intensities(file='ref.list', spectrum_id='ref_ave',
heteronuc='NE1', proton='HE1')
spectrum.read_intensities(file='sat.list', spectrum_id='sat_ave',
heteronuc='N', proton='HN')
@@ -179,21 +182,24 @@
In this example the errors where measured from the base plain noise. The
Sparky\index{software!Sparky} RMSD\index{RMSD} function was used to estimate
the maximal noise levels across the spectrum in regions containing no peaks.
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}
+\begin{lstlisting}[firstnumber=21]
+# Set the errors.
spectrum.baseplane_rmsd(error=3600, spectrum_id='ref_ave')
spectrum.baseplane_rmsd(error=3000, spectrum_id='sat_ave')
\end{lstlisting}
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}
+\begin{lstlisting}[firstnumber=25]
+# 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)
\end{lstlisting}
There are many other ways of setting the errors, for example via spectrum
duplication, triplication, etc. See the documentation for the
\uf{spectrum.error\_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}
+\begin{lstlisting}[firstnumber=29]
+# Peak intensity error analysis.
spectrum.error_analysis()
\end{lstlisting}
@@ -205,7 +211,8 @@
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}
+\begin{lstlisting}[firstnumber=32]
+# Deselect unresolved spins.
deselect.read(name, file='unresolved', res_num_col=1, spin_name_col=2)
\end{lstlisting}
@@ -220,7 +227,8 @@
At this point the NOE can be calculated. The user function
-\begin{lstlisting}
+\begin{lstlisting}[firstnumber=35]
+# Calculate the NOEs.
calc()
\end{lstlisting}
@@ -236,7 +244,8 @@
\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}
+\begin{lstlisting}[firstnumber=38]
+# Save the NOEs.
value.write(param='noe', file='noe.out', force=True)
\end{lstlisting}
@@ -275,7 +284,8 @@
Any two dimensional data set can be plotted in relax in conjunction with the
program
\href{http://plasma-gate.weizmann.ac.il/Grace/}{Grace}\index{software!Grace|textbf}.
The program is also known as Xmgrace and was previously known as ACE/gr or
Xmgr. The highly flexible relax user function \uf{grace.write} is capable of
producing 2D plots of any x-y data sets. The three commands
-\begin{lstlisting}
+\begin{lstlisting}[firstnumber=41]
+# Create Grace files.
grace.write(y_data_type='ref', file='ref.agr', force=True)
grace.write(y_data_type='sat', file='sat.agr', force=True)
grace.write(y_data_type='noe', file='noe.agr', force=True)
@@ -283,13 +293,14 @@
will create three separate plots of the peak intensity of the reference and
saturated spectra as well as the NOE. The x-axis in all three defaults to
the residue number. As the x and y-axes can be any parameter the command
-\begin{lstlisting}
+\begin{lstlisting}[numbers=none]
grace.write(x_data_type='ref', y_data_type='sat', file='ref_vs_sat.agr',
force=True)
\end{lstlisting}
would create a plot of the reference verses the saturated intensity with one
point per residue. Returning to the sample script three Grace data files are
created \file{ref.agr}, \file{sat.agr}, and \file{noe.agr} and placed in the
default directory \directory{./grace}. These can be visualised by opening
the file within Grace. However relax will do that for you with the commands
-\begin{lstlisting}
+\begin{lstlisting}[firstnumber=46]
+# View the Grace files.
grace.view(file='ref.agr')
grace.view(file='sat.agr')
grace.view(file='noe.agr')
r20222 - /trunk/docs/latex/noe.tex