Author: bugman
Date: Thu Jun 20 18:23:24 2013
New Revision: 20241
URL: http://svn.gna.org/viewcvs/relax?rev=20241&view=rev
Log:
Fixed some out of data script code for the relaxation curve-fitting chapter
of the user manual.
Modified:
trunk/docs/latex/curvefit.tex
Modified: trunk/docs/latex/curvefit.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/curvefit.tex?rev=20241&r1=20240&r2=20241&view=diff
==============================================================================
--- trunk/docs/latex/curvefit.tex (original)
+++ trunk/docs/latex/curvefit.tex Thu Jun 20 18:23:24 2013
@@ -298,19 +298,29 @@
\subsection{Relax-fit script mode -- loading the data}
-To load the peak intensities\index{peak!intensity} into relax the user
function \uf{spectrum.read\_intensities} is executed. Important keyword
arguments to this command are the file name and directory, the spectrum
identification string and the relaxation time period of the experiment in
seconds. By default the file format will be automatically detected.
Currently Sparky\index{software!Sparky}, XEasy\index{software!XEasy},
NMRView\index{software!NMRView}, and generic columnar formatted peak lists
are supported. To be able to import any other type of format please send an
email to the relax development mailing list\index{mailing list!relax-devel}
with the details of the format. Adding support for new formats is trivial.
The following series of commands -- an expansion of the \prompt{for} loop in
the sample script -- will load peak intensities from six different relaxation
periods, four of which have been duplicated, from Sparky peak lists with the
peak heights in the 10$^\textrm{th}$ column.
+To load the peak intensities\index{peak!intensity} into relax the
\uf{spectrum.read\_intensities} and \uf{relax\_fit.relax\_times} user
functions are executed. Important keyword arguments for these user functions
are the file name and directory, the spectrum identification string and the
relaxation time period of the experiment in seconds. By default the file
format will be automatically detected. Currently
Sparky\index{software!Sparky}, XEasy\index{software!XEasy},
NMRView\index{software!NMRView}, and generic columnar formatted peak lists
are supported. To be able to import any other type of format please send an
email to the relax development mailing list\index{mailing list!relax-devel}
with the details of the format. Adding support for new formats is trivial.
The following series of commands -- an expansion of the \prompt{for} loop in
the sample script -- will load peak intensities from six different relaxation
periods, four of which have been duplicated, from Sparky peak lists with the
peak heights in the 10$^\textrm{th}$ column.
\begin{lstlisting}[numbers=none]
-spectrum.read_intensities('T2_ncyc1.list', spectrum_id='1',
relax_time=0.0176, int_col=10)
-spectrum.read_intensities('T2_ncyc1b.list', spectrum_id='1b',
relax_time=0.0176, int_col=10)
-spectrum.read_intensities('T2_ncyc2.list', spectrum_id='2',
relax_time=0.0352, int_col=10)
-spectrum.read_intensities('T2_ncyc4.list', spectrum_id='4',
relax_time=0.0704, int_col=10)
-spectrum.read_intensities('T2_ncyc4b.list', spectrum_id='4b',
relax_time=0.0704, int_col=10)
-spectrum.read_intensities('T2_ncyc6.list', spectrum_id='6',
relax_time=0.1056, int_col=10)
-spectrum.read_intensities('T2_ncyc9.list', spectrum_id='9',
relax_time=0.1584, int_col=10)
-spectrum.read_intensities('T2_ncyc9b.list', spectrum_id='9b',
relax_time=0.1584, int_col=10)
-spectrum.read_intensities('T2_ncyc11.list', spectrum_id='11',
relax_time=0.1936, int_col=10)
-spectrum.read_intensities('T2_ncyc11b.list', spectrum_id='11b',
relax_time=0.1936, int_col=10)
+spectrum.read_intensities('T2_ncyc1.list', spectrum_id='1', int_col=10)
+relax_fit.relax_time(spectrum_id='1', time=0.0176)
+spectrum.read_intensities('T2_ncyc1b.list', spectrum_id='1b', int_col=10)
+relax_fit.relax_time(spectrum_id='1b', time=0.0176)
+spectrum.read_intensities('T2_ncyc2.list', spectrum_id='2', int_col=10)
+relax_fit.relax_time(spectrum_id='2', time=0.0352)
+spectrum.read_intensities('T2_ncyc4.list', spectrum_id='4', int_col=10)
+relax_fit.relax_time(spectrum_id='4', time=0.0704)
+spectrum.read_intensities('T2_ncyc4b.list', spectrum_id='4b', int_col=10)
+relax_fit.relax_time(spectrum_id='4b', time=0.0704)
+spectrum.read_intensities('T2_ncyc6.list', spectrum_id='6', int_col=10)
+relax_fit.relax_time(spectrum_id='6', time=0.1056)
+spectrum.read_intensities('T2_ncyc9.list', spectrum_id='9', int_col=10)
+relax_fit.relax_time(spectrum_id='9', time=0.1584)
+spectrum.read_intensities('T2_ncyc9b.list', spectrum_id='9b', int_col=10)
+relax_fit.relax_time(spectrum_id='9b', time=0.1584)
+spectrum.read_intensities('T2_ncyc11.list', spectrum_id='11', int_col=10)
+relax_fit.relax_time(spectrum_id='11', time=0.1936)
+spectrum.read_intensities('T2_ncyc11b.list', spectrum_id='11b', int_col=10)
+relax_fit.relax_time(spectrum_id='11b', time=0.1936)
\end{lstlisting}
The replicated spectra a set up with the commands
r20241 - /trunk/docs/latex/curvefit.tex