Author: bugman
Date: Thu Jun 20 11:58:27 2013
New Revision: 20228
URL: http://svn.gna.org/viewcvs/relax?rev=20228&view=rev
Log:
Converted all of the Consistency testing 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/consistency_tests.tex
Modified: trunk/docs/latex/consistency_tests.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/consistency_tests.tex?rev=20228&r1=20227&r2=20228&view=diff
==============================================================================
--- trunk/docs/latex/consistency_tests.tex (original)
+++ trunk/docs/latex/consistency_tests.tex Thu Jun 20 11:58:27 2013
@@ -63,94 +63,94 @@
The following script can be found in the \directory{sample\_scripts}
directory.
-\begin{exampleenv}
-"""Script for consistency testing. \\
- \\
-Severe artifacts can be introduced if model-free analysis is performed from
inconsistent multiple magnetic field datasets. The use of simple tests as
validation tools for the consistency assessment can help avoid such problems
in order to extract more reliable information from spin relaxation
experiments. In particular, these tests are useful for detecting
inconsistencies arising from R2 data. Since such inconsistencies can yield
artifactual Rex parameters within model-free analysis, these tests should be
use routinely prior to any analysis such as model-free calculations. \\
- \\
-This script will allow one to calculate values for the three consistency
tests J(0), F\_eta and F\_R2. Once this is done, qualitative analysis can be
performed by comparing values obtained at different magnetic fields.
Correlation plots and histograms are useful tools for such comparison, such
as presented in Morin \& Gagne (2009a) J. Biomol. NMR, 45: 361-372. \\
- \\
- \\
-References \\
-========== \\
- \\
-The description of the consistency testing approach: \\
- \\
- Morin \& Gagne (2009a) Simple tests for the validation of multiple field
spin relaxation data. J. Biomol. NMR, 45: 361-372.
http://dx.doi.org/10.1007/s10858-009-9381-4 \\
- \\
-The origins of the equations used in the approach: \\
- \\
- J(0): \\
- Farrow et al. (1995) Spectral density function mapping using 15N
relaxation data exclusively. J. Biomol. NMR, 6: 153-162.
http://dx.doi.org/10.1007/BF00211779 \\
-
- F\_eta: \\
- Fushman et al. (1998) Direct measurement of 15N chemical shift
anisotropy in solution. J. Am. Chem. Soc., 120: 10947-10952.
http://dx.doi.org/10.1021/ja981686m \\
-
- F\_R2: \\
- Fushman et al. (1998) Direct measurement of 15N chemical shift
anisotropy in solution. J. Am. Chem. Soc., 120: 10947-10952.
http://dx.doi.org/10.1021/ja981686m \\
- \\
-A study where consistency tests were used: \\
- \\
- Morin \& Gagne (2009) NMR dynamics of PSE-4 beta-lactamase: An interplay
of ps-ns order and us-ms motions in the active site. Biophys. J., 96:
4681-4691. http://dx.doi.org/10.1016/j.bpj.2009.02.068 \\
-""" \\
- \\
-\# Create the run. \\
-name = `consistency' \\
-pipe.create(name, `ct') \\
- \\
-\# Set up the 15N spins. \\
-sequence.read(`noe.600.out', res\_num\_col=1) \\
-spin.name(name=`N') \\
-spin.element(element=`N') \\
-spin.isotope(isotope=`15N', spin\_id=`@N') \\
- \\
-\# Load the 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 the 1H spins for the magnetic dipole-dipole 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') \\
- \\
-\# Set the angle between the 15N-1H vector and the principal axis of the 15N
chemical shift tensor \\
-value.set(val=15.7, param=`orientation') \\
- \\
-\# Set the approximate correlation time. \\
-value.set(val=13 * 1e-9, param=`tc') \\
- \\
-\# Set the frequency. \\
-consistency\_tests.set\_frq(frq=600.0 * 1e6) \\
- \\
-\# Consistency tests. \\
-calc() \\
- \\
-\# Monte Carlo simulations. \\
-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=`f\_eta', file=`f\_eta.agr', force=True) \\
-grace.write(y\_data\_type=`f\_r2', file=`f\_r2.agr', force=True) \\
- \\
-\# View the grace files. \\
-grace.view(file=`j0.agr') \\
-grace.view(file=`f\_eta.agr') \\
-grace.view(file=`f\_r2.agr') \\
- \\
-\# Finish. \\
-results.write(file=`results', force=True) \\
-state.save(`save', force=True)
-\end{exampleenv}
+\begin{lstlisting}
+""" Script for consistency testing.
+
+Severe artifacts can be introduced if model-free analysis is performed from
inconsistent multiple magnetic field datasets. The use of simple tests as
validation tools for the consistency assessment can help avoid such problems
in order to extract more reliable information from spin relaxation
experiments. In particular, these tests are useful for detecting
inconsistencies arising from R2 data. Since such inconsistencies can yield
artifactual Rex parameters within model-free analysis, these tests should be
use routinely prior to any analysis such as model-free calculations.
+
+This script will allow one to calculate values for the three consistency
tests J(0), F_eta and F_R2. Once this is done, qualitative analysis can be
performed by comparing values obtained at different magnetic fields.
Correlation plots and histograms are useful tools for such comparison, such
as presented in Morin & Gagne (2009a) J. Biomol. NMR, 45: 361-372.
+
+
+References
+==========
+
+The description of the consistency testing approach:
+
+ Morin & Gagne (2009a) Simple tests for the validation of multiple field
spin relaxation data. J. Biomol. NMR, 45: 361-372.
U{http://dx.doi.org/10.1007/s10858-009-9381-4}
+
+The origins of the equations used in the approach:
+
+ J(0):
+ Farrow et al. (1995) Spectral density function mapping using 15N
relaxation data exclusively. J. Biomol. NMR, 6: 153-162.
U{http://dx.doi.org/10.1007/BF00211779}
+
+ F_eta:
+ Fushman et al. (1998) Direct measurement of 15N chemical shift
anisotropy in solution. J. Am. Chem. Soc., 120: 10947-10952.
U{http://dx.doi.org/10.1021/ja981686m}
+
+ F_R2:
+ Fushman et al. (1998) Direct measurement of 15N chemical shift
anisotropy in solution. J. Am. Chem. Soc., 120: 10947-10952.
U{http://dx.doi.org/10.1021/ja981686m}
+
+A study where consistency tests were used:
+
+ Morin & Gagne (2009) NMR dynamics of PSE-4 beta-lactamase: An interplay
of ps-ns order and us-ms motions in the active site. Biophys. J., 96:
4681-4691. U{http://dx.doi.org/10.1016/j.bpj.2009.02.068}
+"""
+
+# Create the data pipe.
+name = 'consistency'
+pipe.create(name, 'ct')
+
+# Set up the 15N spins.
+sequence.read('noe.600.out', res_num_col=1)
+spin.name(name='N')
+spin.element(element='N')
+spin.isotope(isotope='15N', spin_id='@N')
+
+# Load the 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 the 1H spins for the magnetic dipole-dipole 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')
+
+# Set the angle between the 15N-1H vector and the principal axis of the 15N
chemical shift tensor
+value.set(val=15.7, param='orientation')
+
+# Set the approximate correlation time.
+value.set(val=13 * 1e-9, param='tc')
+
+# Set the frequency.
+consistency_tests.set_frq(frq=600.0 * 1e6)
+
+# Consistency tests.
+calc()
+
+# Monte Carlo simulations.
+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='f_eta', file='f_eta.agr', force=True)
+grace.write(y_data_type='f_r2', file='f_r2.agr', force=True)
+
+# View the grace files.
+grace.view(file='j0.agr')
+grace.view(file='f_eta.agr')
+grace.view(file='f_r2.agr')
+
+# Finish.
+results.write(file='results', force=True)
+state.save('save', force=True)
+\end{lstlisting}
This is similar in spirit to the reduced spectral density mapping sample
script (Chapter~\ref{ch: J(w) mapping} on page~\pageref{ch: J(w) mapping}).
@@ -162,24 +162,28 @@
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=`ct')
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=31]
+# Create the data pipe.
+name = 'consistency'
+pipe.create(name, 'ct')
+\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=35]
+# Set up the 15N spins.
+sequence.read('noe.600.out', res_num_col=1)
+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=46]
+# Generate the 1H spins for the magnetic dipole-dipole interaction.
+sequence.attach_protons()
+\end{lstlisting}
This is needed to define the magnetic dipole-dipole interaction which
governs relaxation.
@@ -192,17 +196,19 @@
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 spin system. Note that
if the relaxation data files contain spin information, then this order is not
important. For this analysis, 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=41]
+# Load the 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}
-consistency\_tests.set\_frq(frq=600.0 * 1e6) \\
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=62]
+# Set the frequency.
+consistency_tests.set_frq(frq=600.0 * 1e6)
+\end{lstlisting}
@@ -213,22 +219,25 @@
Prior to calculating the $J(0)$, $F_\eta$, and $F_{R_2}$ 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=49]
+# 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=53]
+# Define the chemical shift relaxation interaction.
+value.set(val=-172 * 1e-6, param='csa')
+\end{lstlisting}
For the angle in degrees between the $^{15}$N-$^1$H vector and the principal
axis of the $^{15}$N chemical shift tensor, the user function call is:
-\begin{exampleenv}
-value.set(val=15.7, param=`orientation')
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=56]
+# Set the angle between the 15N-1H vector and the principal axis of the 15N
chemical shift tensor
+value.set(val=15.7, param='orientation')
+\end{lstlisting}
% Calculation and error propagation.
@@ -238,18 +247,20 @@
Optimisation for this analysis is not needed as this is a direct
calculation. Therefore the $J(0)$, $F_\eta$, and $F_{R_2}$ values are simply
calculated with the call:
-\begin{exampleenv}
-calc()
-\end{exampleenv}
+\begin{lstlisting}[firstnumber=65]
+# Consistency tests.
+calc()
+\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=68]
+# Monte Carlo simulations.
+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.
r20228 - /trunk/docs/latex/consistency_tests.tex