Author: bugman
Date: Mon Aug 26 11:02:20 2013
New Revision: 20685
URL: http://svn.gna.org/viewcvs/relax?rev=20685&view=rev
Log:
Merged revisions 20682-20684 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r20682 | bugman | 2013-08-26 09:43:18 +0200 (Mon, 26 Aug 2013) | 8 lines
Updated the nmrPipe processing script in the relax user manual.
This is in response to the post by Troels Linnet at
http://thread.gmane.org/gmane.science.nmr.relax.user/1520.
The text has also been expanded to better explain spectral processing.
........
r20683 | bugman | 2013-08-26 10:47:08 +0200 (Mon, 26 Aug 2013) | 3 lines
Improvements for the description of the NMRPipe processing script in the
R1/R2 chapter of the user manual.
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r20684 | bugman | 2013-08-26 11:01:16 +0200 (Mon, 26 Aug 2013) | 3 lines
LaTeX fix for the curvefit chapter of the user manual.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/docs/latex/curvefit.tex
Propchange: branches/relax_disp/
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--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Aug 26 11:02:20 2013
@@ -1,1 +1,1 @@
-/trunk:1-20675
+/trunk:1-20684
Modified: branches/relax_disp/docs/latex/curvefit.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/curvefit.tex?rev=20685&r1=20684&r2=20685&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/curvefit.tex (original)
+++ branches/relax_disp/docs/latex/curvefit.tex Mon Aug 26 11:02:20 2013
@@ -84,7 +84,6 @@
Here is an example NMRPipe script designed for optimal relaxation rate
extraction:
-
\begin{lstlisting}[language=csh]
#!/bin/csh
@@ -101,16 +100,34 @@
| nmrPipe -fn ZF -size 8192 \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 $PHASE -p1 0.0 -di -verb \
-| nmrPipe -fn EXT -left -sw \
| nmrPipe -fn TP \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
| nmrPipe -fn ZF -size 8192 \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di -verb \
+| nmrPipe -fn TP \
+| nmrPipe -fn POLY -auto \
+| nmrPipe -fn EXT -left -sw \
+| nmrPipe -out ft/$FILEROOT.dat -ov
+\end{lstlisting}
+
+The script is run by suppling the FILEROOT value as a command line option so
if the script is called \file{nmrpipe.sh} and the \file{var2pipe} or
\file{bruk2pipe} processed file \file{R1\_ncyc4.fid} is in the
\directory{fid} directory, you would run:
+\begin{lstlisting}[language=bash,numbers=none]
+$ ./nmrpipe.sh R1_ncyc4
+\end{lstlisting}
+
+The \directory{ft} directory must exist for this script to execute.
+Different experiment specific options may be needed such as:
+\begin{lstlisting}[language=csh,numbers=none]
| nmrPipe -fn REV \
-| nmrPipe -fn TP \
-| nmrPipe -out ft/$FILEROOT.dat -ov
-\end{lstlisting}
+| nmrPipe -fn FT -neg \
+| nmrPipe -fn PS -rs 2.5 \
+\end{lstlisting}
+
+The script should be changed for different phasing, first point scaling, a
polynomial baseline correction added in the direct dimension or removed from
the indirect dimension, solvent suppression removed or changed, and the
window functions modified for optimal spectral quality.
+Each system and spectrum is different, so it is recommended that to find the
optimal processing that each part of the script be removed and re-added
one-by-one between processing and checking of the resultant spectrum.
+Note that the extraction at the end after the polynomial baseline correction
in the indirect dimension is important as the baseline correction often
displays a much better performance when the empty part of the spectrum is
used in the calculation.
+
% Measuring peak intensities.
r20685 - in /branches/relax_disp: ./ docs/latex/curvefit.tex