Author: bugman
Date: Thu May 1 17:11:06 2008
New Revision: 6049
URL: http://svn.gna.org/viewcvs/relax?rev=6049&view=rev
Log:
Changed all index entries of 'computer programs' to 'software'.
Modified:
1.3/docs/latex/curvefit.tex
1.3/docs/latex/data_analysis.tex
1.3/docs/latex/install.tex
1.3/docs/latex/noe.tex
Modified: 1.3/docs/latex/curvefit.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/curvefit.tex?rev=6049&r1=6048&r2=6049&view=diff
==============================================================================
--- 1.3/docs/latex/curvefit.tex (original)
+++ 1.3/docs/latex/curvefit.tex Thu May 1 17:11:06 2008
@@ -95,7 +95,7 @@
\example{structure.load\_spins(spin\_id=`@N')}
-To load the peak intensities\index{peak!intensity} into relax the user
function \texttt{relax\_fit.read} is executed. Two important keyword
arguments to this command are the file name and the relaxation time period of
the experiment in seconds. It is assumed that the file format is that of a
Sparky\index{computer programs!Sparky} peak list. Using the format argument,
this can be changed to XEasy\index{computer programs!XEasy} text window
output format. 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 will load peak intensities from six
different relaxation periods, four of which have been duplicated
+To load the peak intensities\index{peak!intensity} into relax the user
function \texttt{relax\_fit.read} is executed. Two important keyword
arguments to this command are the file name and the relaxation time period of
the experiment in seconds. It is assumed that the file format is that of a
Sparky\index{software!Sparky} peak list. Using the format argument, this can
be changed to XEasy\index{software!XEasy} text window output format. 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 will load peak intensities from six different relaxation periods,
four of which have been duplicated
\begin{exampleenv}
relax\_fit.read(file=`T2\_ncyc1.list', relax\_time=0.0176) \\
Modified: 1.3/docs/latex/data_analysis.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/data_analysis.tex?rev=6049&r1=6048&r2=6049&view=diff
==============================================================================
--- 1.3/docs/latex/data_analysis.tex (original)
+++ 1.3/docs/latex/data_analysis.tex Thu May 1 17:11:06 2008
@@ -205,7 +205,7 @@
\begin{figure}
\centerline{\includegraphics[width=0.8\textwidth, bb=0 0 792
612]{images/noe.eps.gz}}
-\caption[NOE plot]{A Grace\index{computer programs!Grace|textbf} plot of the
NOE value and error against the residue number. This is an example of the
output of the user function \texttt{grace.write()}.}\label{fig: NOE plot}
+\caption[NOE plot]{A Grace\index{software!Grace|textbf} plot of the NOE
value and error against the residue number. This is an example of the output
of the user function \texttt{grace.write()}.}\label{fig: NOE plot}
\end{figure}
Modified: 1.3/docs/latex/install.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/install.tex?rev=6049&r1=6048&r2=6049&view=diff
==============================================================================
--- 1.3/docs/latex/install.tex (original)
+++ 1.3/docs/latex/install.tex Thu May 1 17:11:06 2008
@@ -118,41 +118,41 @@
% Grace.
\subsection{Grace}
-\index{computer programs!Grace|textbf}
+\index{software!Grace|textbf}
Grace is a program for plotting two dimensional data sets in a professional
looking manner. It is used to visualise parameter values. It can be
downloaded from
\href{http://plasma-gate.weizmann.ac.il/Grace/}{http://plasma-gate.weizmann.ac.il/Grace/}.
% OpenDX.
\subsection{OpenDX}
-\index{computer programs!OpenDX|textbf}
+\index{software!OpenDX|textbf}
Version 4.1.3 or compatible. OpenDX is used for viewing the output of the
space mapping function and is executed by passing the command \texttt{dx} to
the command line with various options. The program is designed for
visualising multidimensional data and can be found at
\href{http://www.opendx.org/}{http://www.opendx.org/}.
% Molmol.
\subsection{Molmol}
-\index{computer programs!Molmol|textbf}
+\index{software!Molmol|textbf}
Molmol is used for viewing the PDB structures loaded into the program and to
display parameter values mapped onto the structure.
% PyMOL.
\subsection{PyMOL}
-\index{computer programs!PyMOL|textbf}
+\index{software!PyMOL|textbf}
PDB structures can also be viewed using PyMOL. Although the mapping of
parameter values onto the structure is not yet supported, this program can be
used to display geometric objects generated by relax for representing
physical concepts such as the diffusion tensor.
% Dasha.
\subsection{Dasha}
-\index{computer programs!Dasha|textbf}
+\index{software!Dasha|textbf}
Dasha is a program used for model-free analysis of NMR relaxation data. It
can be used as an optimisation engine to replace the minimisation algorithms
implemented within relax.
% Modelfree4.
\subsection{Modelfree4}
-\index{computer programs!Modelfree4|textbf}
+\index{software!Modelfree4|textbf}
Art Palmer's Modelfree4 program is also designed for model-free analysis and
can be used as an optimisation engine to replace relax's high precision
minimisation algorithms.
Modified: 1.3/docs/latex/noe.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/noe.tex?rev=6049&r1=6048&r2=6049&view=diff
==============================================================================
--- 1.3/docs/latex/noe.tex (original)
+++ 1.3/docs/latex/noe.tex Thu May 1 17:11:06 2008
@@ -106,7 +106,7 @@
noe.read(file=`sat.list', spectrum\_type=`sat')
\end{exampleenv}
-load the peak heights\index{peak!height} of the reference and saturated NOE
experiments (although the volume\index{peak!volume} could be used instead).
The keyword argument \texttt{format} has not been specified hence the default
format of a Sparky\index{computer programs!Sparky} peak list (saved after
typing \texttt{`lt'}) is assumed. If the program XEasy\index{computer
programs!XEasy} was used to analyse the spectra the argument
\texttt{format=`xeasy'} is necessary. The first column of the file should be
the Sparky assignment string and it is assumed that the 4$^\textrm{th}$
column contains either the peak height or peak volume. If you have any other
format you would like read by relax please send an email to the relax
development mailing list\index{mailing list!relax-devel} detailing the
software used, the format of the file (specifically where the residue number
and peak intensity\index{peak!intensity} are located), and possibly attaching
an example of the file itself.
+load the peak heights\index{peak!height} of the reference and saturated NOE
experiments (although the volume\index{peak!volume} could be used instead).
The keyword argument \texttt{format} has not been specified hence the default
format of a Sparky\index{software!Sparky} peak list (saved after typing
\texttt{`lt'}) is assumed. If the program XEasy\index{software!XEasy} was
used to analyse the spectra the argument \texttt{format=`xeasy'} is
necessary. The first column of the file should be the Sparky assignment
string and it is assumed that the 4$^\textrm{th}$ column contains either the
peak height or peak volume. If you have any other format you would like read
by relax please send an email to the relax development mailing
list\index{mailing list!relax-devel} detailing the software used, the format
of the file (specifically where the residue number and peak
intensity\index{peak!intensity} are located), and possibly attaching an
example of the file itself.
@@ -194,7 +194,7 @@
\section{Viewing the results}
-Any two dimensional data set can be plotted in relax in conjunction with the
program \href{http://plasma-gate.weizmann.ac.il/Grace/}{Grace}\index{computer
programs!Grace|textbf}. The program is also known as Xmgrace and was
previously known as ACE/gr or Xmgr. The highly flexible relax user function
\texttt{grace.write} is capable of producing 2D plots of any x-y data sets.
The three commands
+Any two dimensional data set can be plotted in relax in conjunction with the
program
\href{http://plasma-gate.weizmann.ac.il/Grace/}{Grace}\index{software!Grace|textbf}.
The program is also known as Xmgrace and was previously known as ACE/gr or
Xmgr. The highly flexible relax user function \texttt{grace.write} is
capable of producing 2D plots of any x-y data sets. The three commands
\begin{exampleenv}
grace.write(y\_data\_type=`ref', file=`ref.agr', force=True) \\
@@ -218,5 +218,5 @@
\begin{figure}
\centerline{\includegraphics[width=0.8\textwidth, bb=0 0 792
612]{images/noe.eps.gz}}
-\caption[NOE plot]{A Grace\index{computer programs!Grace|textbf} plot of the
NOE value and error against the residue number. This is an example of the
output of the user function \texttt{grace.write()}.}\label{fig: NOE plot}
+\caption[NOE plot]{A Grace\index{software!Grace|textbf} plot of the NOE
value and error against the residue number. This is an example of the output
of the user function \texttt{grace.write()}.}\label{fig: NOE plot}
\end{figure}
r6049 - in /1.3/docs/latex: curvefit.tex data_analysis.tex install.tex noe.tex