Author: bugman
Date: Fri Sep 6 16:27:40 2013
New Revision: 20907
URL: http://svn.gna.org/viewcvs/relax?rev=20907&view=rev
Log:
Updated the user manual for the relax_disp.exp_type user function changes.
The script in the prompt/script UI section of the dispersion chapter needed
to be updated.
Modified:
branches/relax_disp/docs/latex/dispersion.tex
Modified: branches/relax_disp/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion.tex?rev=20907&r1=20906&r2=20907&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion.tex (original)
+++ branches/relax_disp/docs/latex/dispersion.tex Fri Sep 6 16:27:40 2013
@@ -685,9 +685,6 @@
spin.name(name='N')
spin.isotope(isotope='15N')
-# Set the relaxation dispersion experiment type.
-relax_disp.exp_type('cpmg fixed')
-
# The spectral data - spectrum ID, peak list file name, CPMG frequency (Hz),
spectrometer frequency in Hertz.
data = [
['500_reference.in', '500_MHz'+sep+'reference.in_sparky',
None, 500e6],
@@ -735,6 +732,9 @@
# Load the peak intensities.
spectrum.read_intensities(file=file, spectrum_id=id, int_method='height')
+ # Set the relaxation dispersion experiment type.
+ relax_disp.exp_type(spectrum_id=id, exp_type='CPMG')
+
# Set the relaxation dispersion CPMG frequencies.
relax_disp.cpmg_frq(spectrum_id=id, cpmg_frq=cpmg_frq)
@@ -879,21 +879,6 @@
will set up the spin information required for loading the peak intensity
data from Sparky peak lists and for the analysis of the dispersion data.
-% Experiment type.
-%~~~~~~~~~~~~~~~~~
-
-\subsection{Dispersion script mode -- experiment type}
-
-The next step is to specify the type of dispersion experiment which was
performed:
-
-\begin{lstlisting}[firstnumber=42]
-# Set the relaxation dispersion experiment type.
-relax_disp.exp_type('cpmg fixed')
-\end{lstlisting}
-
-See the \uf{relax\_disp.exp\_type} user function on page~\pageref{uf:
relax_disp.exp_type} for a list of all the dispersion experiment types which
are currently supported.
-
-
% Loading the data.
%~~~~~~~~~~~~~~~~~~
@@ -901,7 +886,7 @@
To load the peak intensities\index{peak!intensity} into relax, a large data
structure is first defined:
-\begin{lstlisting}[firstnumber=45]
+\begin{lstlisting}[firstnumber=42]
# The spectral data - spectrum ID, peak list file name, CPMG frequency (Hz),
spectrometer frequency in Hertz.
data = [
['500_reference.in', '500_MHz'+sep+'reference.in_sparky',
None, 500e6],
@@ -949,7 +934,7 @@
The Python \pycode{for} loop starts with the lines:
-\begin{lstlisting}[firstnumber=87]
+\begin{lstlisting}[firstnumber=84]
# Loop over the spectra.
for id, file, cpmg_frq, H_frq in data:
\end{lstlisting}
@@ -958,12 +943,21 @@
The first user function in the block loads the peak intensity data from the
peak lists:
-\begin{lstlisting}[firstnumber=89]
+\begin{lstlisting}[firstnumber=86]
# Load the peak intensities.
spectrum.read_intensities(file=file, spectrum_id=id, int_method='height')
\end{lstlisting}
-This assumes that peak heights were measured. All data will be tagged with
the given ID string. For examples of peak list formats supported by relax,
see Section~\ref{sect: Rx data loading} on page~\pageref{sect: Rx data
loading}. The next user function sets the CPMG frequencies for each spectrum:
+This assumes that peak heights were measured. All data will be tagged with
the given ID string. For examples of peak list formats supported by relax,
see Section~\ref{sect: Rx data loading} on page~\pageref{sect: Rx data
loading}.
+The next step is to specify the dispersion experiment type for each spectrum:
+
+\begin{lstlisting}[firstnumber=89]
+ # Set the relaxation dispersion experiment type.
+ relax_disp.exp_type(spectrum_id=id, exp_type='CPMG')
+\end{lstlisting}
+
+This can either be \pycode{`CPMG'} or \pycode{`R1rho'}.
+The next user function sets the CPMG frequencies for each spectrum:
\begin{lstlisting}[firstnumber=92]
# Set the relaxation dispersion CPMG frequencies.
r20907 - /branches/relax_disp/docs/latex/dispersion.tex