Author: bugman
Date: Tue Mar 28 04:09:24 2006
New Revision: 2418
URL: http://svn.gna.org/viewcvs/relax?rev=2418&view=rev
Log:
All the new lines from the end of the 'exampleenv' environments in the manual
have been removed.
Modified:
1.2/docs/latex/data_analysis.tex
1.2/docs/latex/intro.tex
1.2/docs/relax.pdf
Modified: 1.2/docs/latex/data_analysis.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/data_analysis.tex?rev=2418&r1=2417&r2=2418&view=diff
==============================================================================
--- 1.2/docs/latex/data_analysis.tex (original)
+++ 1.2/docs/latex/data_analysis.tex Tue Mar 28 04:09:24 2006
@@ -70,7 +70,7 @@
results.write(name, file=`results', dir=None, force=1) \\
\\
\# Save the program state. \\
-state.save(`save', force=1) \\
+state.save(`save', force=1)
\end{exampleenv}
@@ -102,7 +102,7 @@
\begin{exampleenv}
noe.read(name, file=`ref.list', spectrum\_type=`ref') \\
-noe.read(name, file=`sat.list', spectrum\_type=`sat') \\
+noe.read(name, file=`sat.list', spectrum\_type=`sat')
\end{exampleenv}
load the peak heights of the reference and saturated NOE experiments
(although the volume could be used instead). The keyword argument
\texttt{format} has not been specified, hence the default format of a
Sparky\index{computer prgrams!Sparky} peak list (saved after typing
\texttt{`lt'}) is assumed. If the program XEasy\index{computer
prgrams!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, while it is assumed that the 4$^\textrm{th}$
column contains either the peak height.
@@ -115,14 +115,14 @@
\begin{exampleenv}
noe.error(name, error=3600, spectrum\_type=`ref') \\
-noe.error(name, error=3000, spectrum\_type=`sat') \\
+noe.error(name, error=3000, spectrum\_type=`sat')
\end{exampleenv}
For the residue G114, the noise levels are significantly increased compared
to the rest of the protein as the peak is located close to the water signal.
The higher errors for this residue are specified by the commands
\begin{exampleenv}
noe.error(name, error=122000, spectrum\_type=`ref', res\_num=114) \\
-noe.error(name, error=8500, spectrum\_type=`sat', res\_num=114) \\
+noe.error(name, error=8500, spectrum\_type=`sat', res\_num=114)
\end{exampleenv}
@@ -186,7 +186,7 @@
\begin{exampleenv}
grace.write(name, y\_data\_type=`ref', file=`ref.agr', force=1) \\
grace.write(name, y\_data\_type=`sat', file=`sat.agr', force=1) \\
-grace.write(name, y\_data\_type=`noe', file=`noe.agr', force=1) \\
+grace.write(name, y\_data\_type=`noe', file=`noe.agr', force=1)
\end{exampleenv}
create three separate plots of the peak intensity of the reference and
saturated spectra as well as the NOE. The x-axis in all three defaults to
the residue number. As the x and y-axes can be any parameter, the command
@@ -198,7 +198,7 @@
\begin{exampleenv}
grace.view(file=`ref.agr') \\
grace.view(file=`sat.agr') \\
-grace.view(file=`noe.agr') \\
+grace.view(file=`noe.agr')
\end{exampleenv}
An example of the output, after modifying the axes, is shown in
figure~\ref{fig: NOE plot}.
@@ -274,7 +274,7 @@
grace.view(file=`rx.agr') \\
\\
\# Save the program state. \\
-state.save(file=name + `.save', force=1) \\
+state.save(file=name + `.save', force=1)
\end{exampleenv}
@@ -285,7 +285,7 @@
\begin{exampleenv}
name = `rx' \\
-run.create(name, `relax\_fit') \\
+run.create(name, `relax\_fit')
\end{exampleenv}
initialise the run by setting the variable \texttt{name} to \texttt{`rx'} to
be used in the calls to user functions and creating a run called
\texttt{`rx'} which is to relaxation curve fitting by the argument
\texttt{`relax\_fit'}. The sequence is extracted from a PDB file using the
same command as the NOE calculation script
@@ -305,7 +305,7 @@
relax\_fit.read(name, file=`T2\_ncyc9.list', relax\_time=0.1584) \\
relax\_fit.read(name, file=`T2\_ncyc9b.list', relax\_time=0.1584) \\
relax\_fit.read(name, file=`T2\_ncyc11.list', relax\_time=0.1936) \\
-relax\_fit.read(name, file=`T2\_ncyc11b.list', relax\_time=0.1936) \\
+relax\_fit.read(name, file=`T2\_ncyc11b.list', relax\_time=0.1936)
\end{exampleenv}
Modified: 1.2/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/intro.tex?rev=2418&r1=2417&r2=2418&view=diff
==============================================================================
--- 1.2/docs/latex/intro.tex (original)
+++ 1.2/docs/latex/intro.tex Tue Mar 28 04:09:24 2006
@@ -22,7 +22,7 @@
\begin{exampleenv}
relax> print "Hello World" \\
Hello World \\
-relax> \\
+relax>
\end{exampleenv}
Or, using relax as a calculator
@@ -30,7 +30,7 @@
\begin{exampleenv}
relax> (1.0 + (2 * 3))/10 \\
0.69999999999999996 \\
-relax> \\
+relax>
\end{exampleenv}
@@ -131,7 +131,7 @@
model\_free.delete \\
model\_free.remove\_tm \\
model\_free.select\_model \\
-relax> model\_free. \\
+relax> model\_free.
\end{exampleenv}
All the objects beginning with an underscore are ``hidden'', they contain
information about the function class\index{function class} and should be
ignored. From the listing the user functions\index{user functions}
\texttt{`copy'}, \texttt{`create\_model'}, \texttt{`delete'},
\texttt{`remove\_tm'}, and \texttt{`select\_model'} contained within
\texttt{`model\_free'} are all visible.
@@ -223,7 +223,7 @@
\\
\# Finish. \\
results.write(run=name, file=`results', force=1) \\
-state.save(`save', force=1) \\
+state.save(`save', force=1)
\end{exampleenv}
Scripting is much more powerful than the prompt as advanced
Python\index{Python} programming can be employed (see the file
`full\_analysis.py' in the `sample\_scripts' directory for an example).
Modified: 1.2/docs/relax.pdf
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/relax.pdf?rev=2418&r1=2417&r2=2418&view=diff
==============================================================================
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r2418 - in /1.2/docs: latex/data_analysis.tex latex/intro.tex relax.pdf