Author: bugman
Date: Thu Jun 20 11:52:09 2013
New Revision: 20226
URL: http://svn.gna.org/viewcvs/relax?rev=20226&view=rev
Log:
Converted all of the J(w) mapping chapter of the user manual to the
lstlisting environment.
This is for all parts of the script UI section of the chapter.
Modified:
trunk/docs/latex/jw_mapping.tex
Modified: trunk/docs/latex/jw_mapping.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/jw_mapping.tex?rev=20226&r1=20225&r2=20226&view=diff
==============================================================================
--- trunk/docs/latex/jw_mapping.tex (original)
+++ trunk/docs/latex/jw_mapping.tex Thu Jun 20 11:52:09 2013
@@ -19,62 +19,65 @@
\section{J(w) mapping script mode -- the sample script}
-\begin{exampleenv}
-\# Create the data pipe. \\
-pipe.create(pipe\_name=`my\_protein', pipe\_type=`jw') \\
- \\
-\# Set up the 15N spins. \\
-sequence.read(file=`noe.600.out', res\_num\_col=1, res\_name\_col=2) \\
-spin.name(name=`N') \\
-spin.element(element=`N') \\
-spin.isotope(isotope=`15N', spin\_id=`@N') \\
- \\
-\# Load the 15N relaxation data. \\
-relax\_data.read(ri\_id=`R1\_600', ri\_type=`R1', frq=600.0*1e6,
file=`r1.600.out', res\_num\_col=1, data\_col=3, error\_col=4) \\
-relax\_data.read(ri\_id=`R2\_600', ri\_type=`R2', frq=600.0*1e6,
file=`r2.600.out', res\_num\_col=1, data\_col=3, error\_col=4) \\
-relax\_data.read(ri\_id=`NOE\_600', ri\_type=`NOE', frq=600.0*1e6,
file=`noe.600.out', res\_num\_col=1, data\_col=3, error\_col=4) \\
- \\
-\# Generate 1H spins for the magnetic dipole-dipole relaxation interaction.
\\
-sequence.attach\_protons() \\
- \\
-\# Define the magnetic dipole-dipole relaxation interaction. \\
-interatom.define(spin\_id1=`@N', spin\_id2=`@H', direct\_bond=True) \\
-interatom.set\_dist(spin\_id1=`@N', spin\_id2=`@H', ave\_dist=1.02 * 1e-10)
\\
- \\
-\# Define the chemical shift relaxation interaction. \\
-value.set(val=-172 * 1e-6, param=`csa') \\
- \\
-\# Select the frequency. \\
-jw\_mapping.set\_frq(frq=600.0 * 1e6) \\
- \\
-\# Reduced spectral density mapping. \\
-calc() \\
- \\
-\# Monte Carlo simulations (well, bootstrapping as this is a calculation and
not a fit!). \\
-monte\_carlo.setup(number=500) \\
-monte\_carlo.create\_data() \\
-calc() \\
-monte\_carlo.error\_analysis() \\
- \\
-\# Create grace files. \\
-grace.write(y\_data\_type=`j0', file=`j0.agr', force=True) \\
-grace.write(y\_data\_type=`jwx', file=`jwx.agr', force=True) \\
-grace.write(y\_data\_type=`jwh', file=`jwh.agr', force=True) \\
- \\
-\# View the grace files. \\
-grace.view(file=`j0.agr') \\
-grace.view(file=`jwx.agr') \\
-grace.view(file=`jwh.agr') \\
- \\
-\# Write out the values. \\
-value.write(param=`j0', file=`j0.txt', force=True) \\
-value.write(param=`jwx', file=`jwx.txt', force=True) \\
-value.write(param=`jwh', file=`jwh.txt', force=True) \\
- \\
-\# Finish. \\
-results.write(file=`results', force=True) \\
-state.save(`save', force=True)
-\end{exampleenv}
+\begin{lstlisting}
+"""Script for reduced spectral density mapping."""
+
+
+# Create the data pipe.
+pipe.create(pipe_name='my_protein', pipe_type='jw')
+
+# Set up the 15N spins.
+sequence.read(file='noe.600.out', res_num_col=1, res_name_col=2)
+spin.name(name='N')
+spin.element(element='N')
+spin.isotope(isotope='15N', spin_id='@N')
+
+# Load the 15N relaxation data.
+relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.0*1e6,
file='r1.600.out', res_num_col=1, data_col=3, error_col=4)
+relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.0*1e6,
file='r2.600.out', res_num_col=1, data_col=3, error_col=4)
+relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0*1e6,
file='noe.600.out', res_num_col=1, data_col=3, error_col=4)
+
+# Generate 1H spins for the magnetic dipole-dipole relaxation interaction.
+sequence.attach_protons()
+
+# Define the magnetic dipole-dipole relaxation interaction.
+interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+interatom.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
+
+# Define the chemical shift relaxation interaction.
+value.set(val=-172 * 1e-6, param='csa')
+
+# Select the frequency.
+jw_mapping.set_frq(frq=600.0 * 1e6)
+
+# Reduced spectral density mapping.
+calc()
+
+# Monte Carlo simulations (well, bootstrapping as this is a calculation and
not a fit!).
+monte_carlo.setup(number=500)
+monte_carlo.create_data()
+calc()
+monte_carlo.error_analysis()
+
+# Create grace files.
+grace.write(y_data_type='j0', file='j0.agr', force=True)
+grace.write(y_data_type='jwx', file='jwx.agr', force=True)
+grace.write(y_data_type='jwh', file='jwh.agr', force=True)
+
+# View the grace files.
+grace.view(file='j0.agr')
+grace.view(file='jwx.agr')
+grace.view(file='jwh.agr')
+
+# Write out the values.
+value.write(param='j0', file='j0.txt', force=True)
+value.write(param='jwx', file='jwx.txt', force=True)
+value.write(param='jwh', file='jwh.txt', force=True)
+
+# Finish.
+results.write(file='results', force=True)
+state.save('save', force=True)
+\end{lstlisting}
@@ -85,24 +88,27 @@
The steps for setting up relax and the data model concept are described in
full detail in Chapter~\ref{ch: data model}. The first step, as for all
analyses in relax, is to create a data pipe for storing all the data:
-\begin{exampleenv}
-pipe.create(pipe\_name=`my\_protein', pipe\_type=`jw')
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=4]
+# Create the data pipe.
+pipe.create(pipe_name='my_protein', pipe_type='jw')
+\end{lstlisting}
Then, in this example, the $^{15}$N spins are created from one of the NOE
relaxation data files (Chapter~\ref{ch: NOE}):
-\begin{exampleenv}
-sequence.read(file=`noe.600.out', res\_num\_col=1, res\_name\_col=2) \\
-spin.name(name=`N') \\
-spin.element(element=`N') \\
-spin.isotope(isotope=`15N', spin\_id=`@N')
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=7]
+# Set up the 15N spins.
+sequence.read(file='noe.600.out', res_num_col=1, res_name_col=2)
+spin.name(name='N')
+spin.element(element='N')
+spin.isotope(isotope='15N', spin_id='@N')
+\end{lstlisting}
Skipping the relaxation data loading, the next part of the analysis is to
create protons attached to the nitrogens for the magnetic dipole-dipole
relaxation interaction:
-\begin{exampleenv}
-sequence.attach\_protons()
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=18]
+# Generate 1H spins for the magnetic dipole-dipole relaxation interaction.
+sequence.attach_protons()
+\end{lstlisting}
This is needed to define the magnetic dipole-dipole interaction which
governs relaxation.
@@ -115,17 +121,19 @@
The loading of relaxation data is straight forward. This is performed prior
to the creation of the proton spins so that the data is loaded only into the
$^{15}$N spin containers and not both spins for each residue. Only data for
a single field strength can be loaded:
-\begin{exampleenv}
-relax\_data.read(ri\_id=`R1\_600', ri\_type=`R1', frq=600.0*1e6,
file=`r1.600.out', res\_num\_col=1, data\_col=3, error\_col=4) \\
-relax\_data.read(ri\_id=`R2\_600', ri\_type=`R2', frq=600.0*1e6,
file=`r2.600.out', res\_num\_col=1, data\_col=3, error\_col=4) \\
-relax\_data.read(ri\_id=`NOE\_600', ri\_type=`NOE', frq=600.0*1e6,
file=`noe.600.out', res\_num\_col=1, data\_col=3, error\_col=4)
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=13]
+# Load the 15N relaxation data.
+relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.0*1e6,
file='r1.600.out', res_num_col=1, data_col=3, error_col=4)
+relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.0*1e6,
file='r2.600.out', res_num_col=1, data_col=3, error_col=4)
+relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0*1e6,
file='noe.600.out', res_num_col=1, data_col=3, error_col=4)
+\end{lstlisting}
The frequency of the data must also be explicitly specified:
-\begin{exampleenv}
-jw\_mapping.set\_frq(frq=600.0 * 1e6) \\
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=28]
+# Select the frequency.
+jw_mapping.set_frq(frq=600.0 * 1e6)
+\end{lstlisting}
@@ -136,16 +144,18 @@
Prior to calculating the $J(\omega)$ values, the physical interactions which
govern relaxation of the spins must be defined. For the magnetic
dipole-dipole relaxation interaction, the user functions are:
-\begin{exampleenv}
-interatom.define(spin\_id1=`@N', spin\_id2=`@H', direct\_bond=True) \\
-interatom.set\_dist(spin\_id1=`@N', spin\_id2=`@H', ave\_dist=1.02 * 1e-10)
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=21]
+# Define the magnetic dipole-dipole relaxation interaction.
+interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+interatom.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
+\end{lstlisting}
For the chemical shift relaxation interaction, the user function call is:
-\begin{exampleenv}
-value.set(val=-172 * 1e-6, param=`csa')
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=25]
+# Define the chemical shift relaxation interaction.
+value.set(val=-172 * 1e-6, param='csa')
+\end{lstlisting}
@@ -156,18 +166,20 @@
Optimisation for this analysis is not needed as this is a direct
calculation. Therefore the $J(\omega)$ values are simply calculated with the
call:
-\begin{exampleenv}
+\begin{lstlisting}[firstnumber=31]
+# Reduced spectral density mapping.
calc()
-\end{exampleenv}
+\end{lstlisting}
The propagation of errors is more complicated. The Monte Carlo simulation
framework of relax can be used to propagate the relaxation data errors to the
spectral density errors. As this is a direct calculation, this collapses
into the standard bootstrapping method. The normal Monte Carlo user
functions can be called:
-\begin{exampleenv}
-monte\_carlo.setup(number=500) \\
-monte\_carlo.create\_data() \\
-calc() \\
-monte\_carlo.error\_analysis()
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=34]
+# Monte Carlo simulations (well, bootstrapping as this is a calculation and
not a fit!).
+monte_carlo.setup(number=500)
+monte_carlo.create_data()
+calc()
+monte_carlo.error_analysis()
+\end{lstlisting}
In this case, the \uf{monte\_carlo.initial\_values} user function call is
not required.
r20226 - /trunk/docs/latex/jw_mapping.tex