r20682 - /trunk/docs/latex/curvefit.tex -- August 26, 2013 - 09:43

Author: bugman
Date: Mon Aug 26 09:43:18 2013
New Revision: 20682

URL: http://svn.gna.org/viewcvs/relax?rev=20682&view=rev
Log:
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.


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=20682&r1=20681&r2=20682&view=diff
==============================================================================
--- trunk/docs/latex/curvefit.tex (original)
+++ trunk/docs/latex/curvefit.tex Mon Aug 26 09:43:18 2013
@@ -101,16 +101,30 @@
 | 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.
+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.