nmrpipe scripts

Some examples of relatively simple scripts for processing NMR data using nmrPipe:

These scripts are to get you started. To optimize the processing for your sample, you
should experiment with different window functions (such as SP, EM, etc.), as well as
phase correction, baseline correction, and linear prediction.

The scripts begin reading a Varian format fid file (filename.var) and finish by
creating a Sparky-format processed spectrum.
===========================================================
Summary of examples:

1) 2-D NOE (States)
2) 2-D TOCSY (States)
3) 2-D N15-H1 HSQC (Sensitivity-enhanced States)
4) 2-D N15-H1 HMQC-JR (TPPI)
5) 2-D N15-H1 HSMQC (TPPI)
6) 2-D C13-H1 HSQC (TPPI)
7) 3-D N15-H1-H1 HSQC-NOE (States, Sensitivity-enhanced States)
8) 3-D N15-H1-H1 HSQC-TOCSY (States, Sensitivity-enhanced States)
9) 3-D C13-H1-H1 HCCH-TOCSY (TPPI)
10) 3-D HNCA (States, Sensitivity-enhanced States)
11) 3-D HACACBCO (TPPI)

===========================================================

1) Homonuclear 2-D NOE :

Example of processing data for a 2-D NOE spectrum
acquired using "States" method for the 2nd dimension.

#!/bin/csh
var2pipe -in ./y2at_wnoe2.var   \
-xN             2048   \
-yN              800   \
-xT             1024   \
-yT              400   \
-xMODE        Complex \
-yMODE        Complex \
-xSW         7800.000 \
-ySW         7800.000 \
-xOBS         500.297 \
-yOBS         500.297 \
-xCAR           4.920 \
-yCAR           4.920 \
-xLAB              H1 \
-yLAB              H1 \
-ndim               2 \
-out ./temp -verb -ov
nmrPipe -in ./temp   \
# | nmrPipe -fn SOL      \
| nmrPipe -fn SP -off 0.02 -end 0.999 -pow 1 -c 1.0         \
| nmrPipe -fn EM -lb 22.0       \
| nmrPipe -fn FT          \
| nmrPipe -fn PS -p0 -45.0 -p1 -117.0 -di         \
| nmrPipe -fn EXT -x1 12.5ppm -xn -0.5ppm -sw -round   \
| nmrPipe -fn TP          \
| nmrPipe -fn ZF -auto         \
| nmrPipe -fn SP -off 0.50 -end 0.999 -pow 1 -c 0.6         \
| nmrPipe -fn EM -lb 1.0   \
| nmrPipe -fn FT         \
| nmrPipe -fn PS -p0 -20.0 -p1 40.0 -di         \
| nmrPipe -fn EXT -x1 12.5ppm -xn -0.5ppm -sw -round   \
| nmrPipe -fn POLY -auto    \
| nmrPipe -fn TP   \
| nmrPipe -fn POLY -auto \
-out ./temp2 -verb -ov
pipe2ucsf temp2 y2at_wnoe2.spa
rm -f temp
rm -f temp2
cp y2at_wnoe2.spa ~/Sparky/Save/

===========================================================
2) Homonuclear 2-D TOCSY :

Example of processing data for a 2-D TOCSY spectrum
acquired using "States" method for the 2nd dimension:

#!/bin/csh
var2pipe -in ./y2at_wtoc2.var   \
-xN             2048   \
-yN              600   \
-xT             1024   \
-yT              300   \
-xMODE        Complex \
-yMODE        Complex \
-xSW         7800.000 \
-ySW         7800.000 \
-xOBS         500.297 \
-yOBS         500.297 \
-xCAR           4.920 \
-yCAR           4.920 \
-xLAB              H1 \
-yLAB              H1 \
-ndim               2 \
-out ./temp -verb -ov
nmrPipe -in ./temp   \
# | nmrPipe -fn SOL      \
| nmrPipe -fn SP -off 0.02 -end 0.99 -pow 1 -c 0.9         \
| nmrPipe -fn EM -lb 22.0     \
| nmrPipe -fn FT          \
| nmrPipe -fn PS -p0 100.0 -p1 -60.0 -di         \
| nmrPipe -fn EXT -x1 12.5ppm -xn -0.5ppm -sw -round   \
| nmrPipe -fn TP          \
| nmrPipe -fn ZF -auto         \
| nmrPipe -fn SP -off 0.5 -end 0.99 -pow 1 -c 0.5         \
| nmrPipe -fn FT         \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di         \
| nmrPipe -fn EXT -x1 12.5ppm -xn -0.5ppm -sw -round   \
| nmrPipe -fn POLY -auto    \
| nmrPipe -fn TP            \
| nmrPipe -fn POLY -auto    \
| nmrPipe -fn TP            \
-out ./temp2 -verb -ov
pipe2ucsf temp2 y2at_wtoc2.spa
rm -f temp
rm -f temp2
cp y2at_wtoc2.spa ~/Sparky/Save/

===========================================================

3) Heteronuclear 2-D HSQC :

For data acquired using Sensitivity-enhanced "States-Tppi" method
for the 2nd dimension, such as with 15N-1H HSQC:

#!/bin/csh
var2pipe -in ./y2at_hsqc1.var   \
-xN             2048   \
-yN              512   \
-xT             1024   \
-yT              256   \
-xMODE        Complex \
-yMODE      Rance-Kay \
-xSW         8500.000 \
-ySW         5000.000 \
-xOBS         500.297 \
-yOBS          50.700 \
-xCAR           4.800 \
-yCAR         121.000 \
-xLAB              H1 \
-yLAB             N15 \
-ndim               2 \
-out ./temp -verb -ov
nmrPipe -in ./temp   \
| nmrPipe -fn SOL      \
| nmrPipe -fn SP -off 0.02 -end 0.999 -pow 1 -c 1.0   \
| nmrPipe -fn EM -lb 22      \
| nmrPipe -fn FT          \
| nmrPipe -fn PS -p0 270.0 -p1 -55.0 -di    \
| nmrPipe -fn TP     \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn SP -off 0.14 -end 0.999 -pow 1 -c 0.5   \
| nmrPipe -fn EM -lb 3    \
| nmrPipe -fn FT         \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di   \
| nmrPipe -fn REV     \
| nmrPipe -fn POLY -auto \
-out ./temp2 -verb -ov
#
pipe2ucsf temp2 y2at_hsqc1.spa
rm -f temp
rm -f temp2
#

==========================================================

4) Heteronuclear 2-D HMQC-JR (HMQC with jump-return water suppression):

For data acquired using TPPI for second dimension:

#!/bin/csh
var2pipe -in ./y2a_hmqcjr_2.var   \
-xN             2048   \
-yN              700   \
-xT             1024   \
-yT              700   \
-xMODE        Complex \
-yMODE        Real     \
-xSW         8500.000 \
-ySW         5000.000 \
-xOBS         500.297 \
-yOBS          50.700 \
-xCAR           4.870 \
-yCAR          121.00 \
-xLAB              H1 \
-yLAB             N15 \
-ndim               2 \
-out ./temp -verb -ov
nmrPipe -in ./temp   \
| nmrPipe -fn NULL    \
| nmrPipe -fn SP -off 0.020 -end 0.99 -pow 1 -c 0.9         \
| nmrPipe -fn EM -lb 20.0   \
| nmrPipe -fn FT          \
| nmrPipe -fn PS -p0 180.0 -p1 0.0 -di         \
| nmrPipe -fn EXT -x1 12.8ppm -xn 5.5ppm -sw -round   \
| nmrPipe -fn TP          \
| nmrPipe -fn ZF -auto         \
| nmrPipe -fn SP -off 0.35 -end 0.98 -pow 2 -c 0.6         \
| nmrPipe -fn EM -lb 6.0   \
| nmrPipe -fn FT -real         \
| nmrPipe -fn PS -p0 -55.0 -p1 470.0           \
| nmrPipe -fn REV -di \
| nmrPipe -fn TP     \
| nmrPipe -fn POLY -auto \
| nmrPipe -fn TP          \
| nmrPipe -fn POLY -auto   \
-out ./temp2 -verb -ov
pipe2ucsf temp2 y2a_hmqcjr_2.spa
rm -f temp
rm -f temp2
cp y2a_hmqcjr_2.spa ~/Sparky/Save/
#

===========================================================

5) Heteronuclear 2-D HSMQC.

For data acquired using TPPI for second dimension:

#!/bin/csh
var2pipe -in ./y2a_hsmqc.var   \
-xN             2048   \
-yN              512   \
-xT             1024   \
-yT              512   \
-xMODE        Complex \
-yMODE        Real     \
-xSW         8500.000 \
-ySW         5000.000 \
-xOBS         500.297 \
-yOBS          50.700 \
-xCAR           4.890 \
-yCAR          117.50 \
-xLAB              H1 \
-yLAB             N15 \
-ndim               2 \
-out ./temp -verb -ov
nmrPipe -in ./temp   \
# | nmrPipe -fn SOL    \
| nmrPipe -fn SP -off 0.02 -end 0.98 -pow 1 -c 0.7         \
| nmrPipe -fn EM -lb 20.0     \
| nmrPipe -fn FT          \
| nmrPipe -fn PS -p0 90.0 -p1 -30.0 -di         \
| nmrPipe -fn EXT -x1 12.6ppm -xn 5.5ppm -sw -round   \
| nmrPipe -fn TP          \
| nmrPipe -fn ZF -auto         \
| nmrPipe -fn SP -off 0.3 -end 0.98 -pow 1 -c 0.5         \
| nmrPipe -fn FT -real         \
| nmrPipe -fn PS -p0 -72.0 -p1 149.0           \
| nmrPipe -fn REV -di \
| nmrPipe -fn TP     \
| nmrPipe -fn POLY -auto \
-out ./temp2 -verb -ov
pipe2ucsf temp2 y2a_hsmqc.spa
rm -f temp
rm -f temp2
cp y2a_hsmqc.spa ~/Sparky/Save/

===========================================================
6) C13-H1 HSQC (2-D) :

For data acquired using "TPPI" method for the 2nd dimension:

#!/bin/csh
var2pipe -in ./peng_10jul01_wt6.var   \
-xN             2048   \
-yN              512   \
-xT             1024   \
-yT              512   \
-xMODE        Complex \
-yMODE        Real     \
-xSW         6000.200 \
-ySW        25160.200 \
-xOBS         500.297 \
-yOBS         125.807 \
-xCAR           4.700 \
-yCAR           70.00 \
-xLAB              H1 \
-yLAB             C13 \
-ndim               2 \
-out ./temp -verb -ov
nmrPipe -in ./temp       \
| nmrPipe -fn NULL       \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
| nmrPipe -fn FT         \
| nmrPipe -fn PS -p0 -25.0 -p1 0.0 -di \
| nmrPipe -fn TP         \
| nmrPipe -fn ZF -auto   \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
| nmrPipe -fn FT -real   \
| nmrPipe -fn PS -p0 0.0 -p1 360.0   \
| nmrPipe -fn REV -di    \
| nmrPipe -fn POLY -auto \
| nmrPipe -fn TP         \
| nmrPipe -fn POLY -auto \
| nmrPipe -fn TP         \
-out ./temp2 -verb -ov
pipe2ucsf temp2 peng_10jul01_wt6.spa
rm -f temp
rm -f temp2
#

===========================================================

7) 3-D HSQC-NOE :

For data acquired using States method for the 2nd dimension (H1)
and sensitivity-enhanced States-TPPI for the 3rd dimension (N15).
Includes baseline correction.

#!/bin/csh
var2pipe -in ./y2at_hqnoe.var   \
-xN             1024   \
-yN              256   \
-zN               64   \
-xT              512   \
-yT              128   \
-zT               32   \
-xMODE        Complex \
-yMODE        Complex \
-zMODE      Rance-Kay \
-xSW         6200.000 \
-ySW         6200.000 \
-zSW         1650.000 \
-xOBS         500.297 \
-yOBS         500.297 \
-zOBS          50.700 \
-xCAR           4.914 \
-yCAR           4.914 \
-zCAR         118.700 \
-xLAB              H1 \
-yLAB              H1 \
-zLAB             N15 \
-ndim               3 \
-aqORD              1 \
-out ./temp_files/test%03d.fid -verb -ov
#
xyz2pipe -in temp_files/test%03d.fid -x -verb \
| nmrPipe -fn SP -off 0.36 -end 0.998 -pow 1 -c 1.0 \
| nmrPipe -fn ZF -auto      \
| nmrPipe -fn FT          \
| nmrPipe -fn PS -p0 -104.0 -p1 0.0      \
| nmrPipe -fn EXT -x1 11.24ppm -xn 5.6ppm -sw -round \
| pipe2xyz -out temp_files/test%03d.ft1 -x        \
#
xyz2pipe -in temp_files/test%03d.ft1 -z -verb \
| nmrPipe -fn SP -off 0.36 -end 0.99 -pow 1 -c 0.6         \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn FT    \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di         \
| nmrPipe -fn REV       \
| pipe2xyz -out temp_files/test%03d.ft2 -z -verb    \
#
xyz2pipe -in temp_files/test%03d.ft2 -y -verb   \
| nmrPipe -fn SP -off 0.36 -end 0.99 -pow 1 -c 0.6        \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn FT      \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di   \
| nmrPipe -fn POLY -auto   \
| pipe2xyz -out temp_files/test%3d.ft3 -y -verb   \
#
xyz2pipe -in temp_files/test%3d.ft3 -x -verb   \
| nmrPipe -fn POLY -auto     \
| pipe2xyz -out temp_files/test%3d.ft4 -x -verb   \
#
xyz2pipe -in temp_files/test%3d.ft4 -z -out spectrum \
#
pipe2ucsf spectrum y2at_hqnoe.spa
cp y2at_hqnoe.spa ~/Sparky/Save/
#
rm -rf temp_files
rm -f spectrum
#

===========================================================

8) 3-D HSQC-TOCSY :

For data acquired using States method for the 2nd dimension (H1)
and sensitivity-enhanced States-TPPI for the 3rd dimension (N15).
Includes baseline correction.

#!/bin/csh
var2pipe -in ./y2at_hqtoc.var   \
-xN             1024   \
-yN              256   \
-zN               64   \
-xT              512   \
-yT              128   \
-zT               32   \
-xMODE        Complex \
-yMODE        Complex \
-zMODE      Rance-Kay \
-xSW         6200.000 \
-ySW         6200.000 \
-zSW         1650.000 \
-xOBS         500.297 \
-yOBS         500.297 \
-zOBS          50.700 \
-xCAR           4.914 \
-yCAR           4.914 \
-zCAR         118.700 \
-xLAB              H1 \
-yLAB              H1 \
-zLAB             N15 \
-ndim               3 \
-aqORD              1 \
-out ./temp_files/test%03d.fid -verb -ov
#
xyz2pipe -in temp_files/test%03d.fid -x -verb \
| nmrPipe -fn SP -off 0.36 -end 0.998 -pow 1 -c 1.0 \
| nmrPipe -fn ZF -auto      \
| nmrPipe -fn FT          \
| nmrPipe -fn PS -p0 -104.0 -p1 0.0      \
| nmrPipe -fn EXT -x1 11.24ppm -xn 5.6ppm -sw -round \
| pipe2xyz -out temp_files/test%03d.ft1 -x        \
#
xyz2pipe -in temp_files/test%03d.ft1 -z -verb \
| nmrPipe -fn SP -off 0.36 -end 0.99 -pow 1 -c 0.6         \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn FT    \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di         \
| nmrPipe -fn REV       \
| pipe2xyz -out temp_files/test%03d.ft2 -z -verb    \
#
xyz2pipe -in temp_files/test%03d.ft2 -y -verb   \
| nmrPipe -fn SP -off 0.36 -end 0.99 -pow 1 -c 0.6        \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn FT      \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di   \
| nmrPipe -fn POLY -auto   \
| pipe2xyz -out temp_files/test%3d.ft3 -y -verb   \
#
xyz2pipe -in temp_files/test%3d.ft3 -x -verb   \
| nmrPipe -fn POLY -auto     \
| pipe2xyz -out temp_files/test%3d.ft4 -x -verb   \
#
xyz2pipe -in temp_files/test%3d.ft4 -z -out spectrum \
#
pipe2ucsf spectrum y2at_hqtoc.spa
cp y2at_hqtoc.spa ~/Sparky/Save/
#
rm -rf temp_files
rm -f spectrum
#

===========================================================

9) 3-D HCCH-TOCSY :

For data acquired using "TPPI" method for the 2nd & 3rd dimensions.
Includes baseline correction.

#!/bin/csh
var2pipe -in ./y2a_hcch.var   \
-xN             1024   \
-yN              256   \
-zN               92   \
-xT              512   \
-yT              256   \
-zT               92   \
-xMODE        Complex \
-yMODE           Real \
-zMODE           Real \
-xSW         5800.000 \
-ySW         5800.000 \
-zSW         8400.000 \
-xOBS         500.297 \
-yOBS         500.297 \
-zOBS         125.800 \
-xCAR           4.914 \
-yCAR           4.914 \
-zCAR           43.10 \
-xLAB              H1 \
-yLAB              H1 \
-zLAB             C13 \
-ndim               3 \
-out ./temp_files/test%03d.fid -verb -ov
xyz2pipe -in temp_files/test%03d.fid -x -verb \
| nmrPipe -fn SP -off 0.36 -end 0.99 -pow 1 -c 1.0         \
# | nmrPipe -fn EM -lb 20.0      \
| nmrPipe -fn ZF -auto      \
| nmrPipe -fn FT          \
| nmrPipe -fn PS -p0 146.0 -p1 0.0 -di         \
| nmrPipe -fn EXT -x1 6.0ppm -xn -0.5ppm -sw -round \
| pipe2xyz -out temp_files/test%03d.ft1 -x        \
#
xyz2pipe -in temp_files/test%03d.ft1 -y -verb \
| nmrPipe -fn SP -off 0.36 -end 0.99 -pow 1 -c 1.0         \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn FT -real   \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di         \
| nmrPipe -fn REV                             \
| pipe2xyz -out temp_files/test%03d.ft2 -y -verb    \
#
xyz2pipe -in temp_files/test%03d.ft2 -z -verb   \
| nmrPipe -fn SP -off 0.36 -end 0.99 -pow 1 -c 1.0        \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn FT -real      \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di   \
| nmrPipe -fn REV                       \
| pipe2xyz -out temp_files/test%3d.ft3 -z -verb   \
#
xyz2pipe -in temp_files/test%3d.ft3 -x -verb   \
| nmrPipe -fn POLY -auto     \
| pipe2xyz -out temp_files/test%3d.ft4 -x -verb   \
#
xyz2pipe -in temp_files/test%3d.ft4 -y -verb   \
| nmrPipe -fn POLY -auto     \
| nmrPipe -fn EXT -x1 6.0ppm -xn -0.5ppm -sw -round \
| pipe2xyz -out temp_files/test%3d.ft5 -y -verb   \
#
xyz2pipe -in temp_files/test%3d.ft5 -z -out spectrum \
#
pipe2ucsf spectrum y2a_hcch.spa
cp y2a_hcch.spa ~/Sparky/Save
#
rm -rf temp_files
rm -f spectrum
#

===========================================================

10) 3-D HNCA :

For data acquired using States method for the 2nd dimension (C13)
and sensitivity-enhanced States-TPPI for the 3rd dimension (N15).
Includes baseline correction.

#!/bin/csh
var2pipe -in ./y2a_hnca.var   \
-xN             1024   \
-yN              128   \
-zN               64   \
-xT              512   \
-yT               64   \
-zT               32   \
-xMODE        Complex \
-yMODE        Complex \
-zMODE      Rance-Kay \
-xSW         7650.000 \
-ySW         4000.000 \
-zSW         1650.200 \
-xOBS         500.297 \
-yOBS         125.800 \
-zOBS          50.700 \
-xCAR           4.915 \
-yCAR          54.000 \
-zCAR         119.200 \
-xLAB              H1 \
-yLAB             C13 \
-zLAB             N15 \
-ndim               3 \
-aqORD              1 \
-out ./temp_files/test%03d.fid -verb -ov
xyz2pipe -in temp_files/test%03d.fid -x -verb \
| nmrPipe -fn SP -off 0.4 -end 0.99 -pow 1 -c 1.0         \
| nmrPipe -fn ZF -auto      \
| nmrPipe -fn FT          \
| nmrPipe -fn PS -p0 -102.0 -p1 0.0      \
| nmrPipe -fn EXT -x1 12.54ppm -xn 5.6ppm -sw -round \
| pipe2xyz -out temp_files/test%03d.ft1 -x        \
#
xyz2pipe -in temp_files/test%03d.ft1 -z -verb \
| nmrPipe -fn SP -off 0.3 -end 0.99 -pow 1 -c 0.6         \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn FT    \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di         \
| pipe2xyz -out temp_files/test%03d.ft2 -z -verb    \
#
xyz2pipe -in temp_files/test%03d.ft2 -y -verb   \
| nmrPipe -fn SP -off 0.3 -end 0.99 -pow 1 -c 0.6        \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn FT      \
| nmrPipe -fn PS -p0 0.0 -p1 -0.0 -di   \
# | nmrPipe -fn POLY -auto    \
| pipe2xyz -out temp_files/test%3d.ft3 -y -verb   \
#
xyz2pipe -in temp_files/test%3d.ft3 -x -verb   \
| nmrPipe -fn POLY -auto     \
| pipe2xyz -out temp_files/test%3d.ft4 -x -verb   \
#
xyz2pipe -in temp_files/test%3d.ft4 -z -out spectrum \
#
pipe2ucsf spectrum y2a_hnca.spa
cp y2a_hnca.spa ~/Sparky/Save/
#
rm -rf temp_files
rm -f spectrum
#

===========================================================

11) 3-D HACACBCO (TPPI in 2nd and 3rd dimensions).
Includes baseline correction.

#!/bin/csh
var2pipe -in ./y2a_hacacbco.var   \
-xN             1024   \
-yN              120   \
-zN               60   \
-xT              512   \
-yT              120   \
-zT               60   \
-xMODE        Complex \
-yMODE           Real \
-zMODE           Real \
-xSW         5000.000 \
-ySW         8400.000 \
-zSW         1950.000 \
-xOBS         500.297 \
-yOBS         125.800 \
-zOBS         125.800 \
-xCAR           4.914 \
-yCAR          43.100 \
-zCAR          172.40 \
-xLAB              H1 \
-yLAB            CACB \
-zLAB              CO \
-ndim               3 \
-out ./temp_files/test%03d.fid -verb -ov
xyz2pipe -in temp_files/test%03d.fid -x -verb \
| nmrPipe -fn SP -off 0.36 -end 0.99 -pow 1 -c 1.0         \
# | nmrPipe -fn EM -lb 20.0      \
| nmrPipe -fn ZF -auto      \
| nmrPipe -fn FT          \
| nmrPipe -fn PS -p0 142.0 -p1 0.0 -di         \
| nmrPipe -fn EXT -x1 6.0ppm -xn 2.5ppm -sw -round \
| pipe2xyz -out temp_files/test%03d.ft1 -x        \
#
xyz2pipe -in temp_files/test%03d.ft1 -y -verb \
| nmrPipe -fn SP -off 0.36 -end 0.99 -pow 1 -c 0.6         \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn FT -real   \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di         \
| nmrPipe -fn REV                             \
| pipe2xyz -out temp_files/test%03d.ft2 -y -verb    \
#
xyz2pipe -in temp_files/test%03d.ft2 -z -verb   \
| nmrPipe -fn SP -off 0.36 -end 0.99 -pow 1 -c 0.6        \
| nmrPipe -fn ZF -auto    \
| nmrPipe -fn FT -real      \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di   \
| nmrPipe -fn REV                       \
| pipe2xyz -out temp_files/test%3d.ft3 -z -verb   \
#
xyz2pipe -in temp_files/test%3d.ft3 -x -verb   \
| nmrPipe -fn POLY -auto     \
| pipe2xyz -out temp_files/test%3d.ft4 -x -verb   \
#
xyz2pipe -in temp_files/test%3d.ft4 -z -out spectrum \
#
pipe2ucsf spectrum y2a_hacacbco.spa
cp y2a_hacacbco.spa ~/Sparky/Save
#
rm -rf temp_files
rm -f spectrum
#

===========================================================