Author: bugman
Date: Thu Jun 20 19:15:47 2013
New Revision: 20243
URL: http://svn.gna.org/viewcvs/relax?rev=20243&view=rev
Log:
Merged revisions 20240-20242 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r20240 | bugman | 2013-06-20 18:10:03 +0200 (Thu, 20 Jun 2013) | 3 lines
Small typo fix for the relaxation curve-fitting chapter of the user manual.
........
r20241 | bugman | 2013-06-20 18:23:24 +0200 (Thu, 20 Jun 2013) | 3 lines
Fixed some out of data script code for the relaxation curve-fitting chapter
of the user manual.
........
r20242 | bugman | 2013-06-20 18:59:56 +0200 (Thu, 20 Jun 2013) | 3 lines
Added a section label to the relaxation curve-fitting chapter of the user
manual.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/docs/latex/curvefit.tex
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Jun 20 19:15:47 2013
@@ -1,1 +1,1 @@
-/trunk:1-20236
+/trunk:1-20242
Modified: branches/relax_disp/docs/latex/curvefit.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/curvefit.tex?rev=20243&r1=20242&r2=20243&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/curvefit.tex (original)
+++ branches/relax_disp/docs/latex/curvefit.tex Thu Jun 20 19:15:47 2013
@@ -275,7 +275,7 @@
\subsection{Relax-fit script mode -- setting up the spin systems}
-The first thing which need to be completed prior to any spin specific
command is to generate the molecule, residue and spin data structures for
storing the spin specific data. In the sample script above this is generated
from a PDB file, however a plain text file with the sequence information can
be used instead (see the \uf{sequence.read} user function on
page~\pageref{uf: sequence.read} for more details). In the case of the
sample script, the command
+The first thing which needs to be completed prior to any spin specific
command is to generate the molecule, residue and spin data structures for
storing the spin specific data. In the sample script above this is generated
from a PDB file, however a plain text file with the sequence information can
be used instead (see the \uf{sequence.read} user function on
page~\pageref{uf: sequence.read} for more details). In the case of the
sample script, the command
\begin{lstlisting}[firstnumber=6]
# Load the backbone amide 15N spins from a PDB file.
@@ -296,21 +296,31 @@
% Loading the data.
%~~~~~~~~~~~~~~~~~~
-\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.
+\subsection{Relax-fit script mode -- loading the data} \label{sect: Rx data
loading}
+
+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
r20243 - in /branches/relax_disp: ./ docs/latex/curvefit.tex