NMRPipe Processing Functions
EXT: Extract Region.

Flag	Argument	Default	Description
`-time`			Extract Time Domain.
`-left`			Extract Left Half.
`-right`			Extract Right Half.
`-mid`			Extract Center Half.
`-pow2`			Round size to nearest power of 2.
`-sw`			Adjust Sweep Width and ppm calibration.
`-round`	`n`	`1`	Round size to nearest N.

Extract Region Coordinates (Valid Units: Pts Hz ppm %):

`-x1`	`xFirst`	`1`	X Extract Range Start.
`-xn`	`xLast`	`XSIZE`	X Extract Range End.
`-y1`	`yFirst`	`1`	Y Extract Range Start.
`-yn`	`yLast`	`YSIZE`	Y Extract Range End.

Notes:
Use negative integers for coords in order to specify limit relative to last point.

EXT extracts a range of points from each vector in the data. Optionally, it can be used to select a range of vectors from within each plane as well.

OPTIONS

-x1 x1
Specifies the location of the first point in range of points to extract, with default units in points. The default value is 1, the first point in the data vector. The valid unit labels are: Pts Hz ppm %. When specifying a location with a unit label, there should be no spaces between the numerical value and the label. If a negative integer value is specified, the location will be interpreted relative to the last point in the data. For example, -x1 -4 specifies a location at point N - 4.

-xn xn
Specifies the location of the last point in range of points to extract, with default units in points. The default value is the last point in the data vector. The valid unit labels are: Pts Hz ppm %. When specifying a location with a unit label, there should be no spaces between the numerical value and the label. If a negative integer value is specified, the location will be interpreted relative to the last point in the data. For example, -xn -2 specifies a location at point N - 2.

-y1 y1
Specifies the location of the first vector in range of vectors to extract, with default units in points. The default value is 1, the first vector in the data plane. The valid unit labels are: Pts Hz ppm %. When specifying a location with a unit label, there should be no spaces between the numerical value and the label. If a negative integer value is specified, the location will be interpreted relative to the last vector in the data. For example, -y1 -4 specifies a location at vector M - 4.

-yn yn
Specifies the location of the last vector in range of vectors to extract, with default units in points. The default value is the last vector in the data plane. The valid unit labels are: Pts Hz ppm %. When specifying a location with a unit label, there should be no spaces between the numerical value and the label. If a negative integer value is specified, the location will be interpreted relative to the last vector in the data. For example, -yn -2 specifies a location at vector M - 2.

-left
Extracts the points in the "left" half of each vector, from points x1 = 1 to xn = N/2. Equivalent to -x1 1 -xn 50%.

-right
Extracts the points in the "right" half of each vector, from points x1 = N/2 + 1 to xn = N.

-mid
Extracts the "center half" each vector, from point x1 = N/4 + 1 to point x2 = x1 + N/2 - 1.

-round N
If this argument is included, the limits of the extract region will be expanded if needed to attempt to make the size of the extracted region an even multiple of N points.

-pow2
If this argument is included, the limits of the extract region will be expanded if needed to attempt to make the size of the extracted region a power of two. p> -sw
By default, only the header values for NDSIZE, the number of points in the given dimension, are adjusted by EXT. If the -sw argument is included, related values in the header will be adjusted to reflect the details of the extracted region, in particular the change in chemical shift calibration information (NDSW, NDCENTER and NDORIG), and the change in the valid number of time-domain points associated with the data (NDTDSIZE and NDAPOD). In the case of frequency domain data, the -sw argument will also update header values NDX1 and NDXN, which record the limits of the extracted region in points.

Note that the -sw option should be used in most all cases. The likely exceptions are schemes which will inverse-process an extracted dimension.

EXAMPLES

In the case of amide-detected data, the most common use of EXT is to extract the range of points where amide-H signals will be found. This is commonly to the "left" of the water signal at the center of the directly detected dimension:

   nmrPipe -in test.fid \
   | nmrPipe  -fn SOL                                  \
   | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5  \
   | nmrPipe  -fn ZF -auto                             \
   | nmrPipe  -fn FT                                   \
   | nmrPipe  -fn PS -p0 43  -p1 0.0 -di               \
   | nmrPipe  -fn EXT -left -sw                        \
   | nmrPipe  -fn TP                                   \
   | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 1.0  \
   | nmrPipe  -fn ZF -auto                             \
   | nmrPipe  -fn FT                                   \
   | nmrPipe  -fn PS -p0 -135 -p1 180 -di              \
   | nmrPipe  -fn TP                                   \
   | nmrPipe  -fn POLY -auto                           \
      -out test.ft2 -verb -ov

The above use of EXT will commonly be adjusted to include a a more specific and narrower range of points, for example:

   | nmrPipe  -fn EXT -x1 11.5ppm -xn 5.5ppm -sw       \

The EXT function can be used in the time-domain to limit the number of points used. Since the starting value -x1 is the first point by default, this option can be left out of the command line in such cases. For example, to transform using only the first 1024 complex points of a larger FID:

   nmrPipe -in test.fid \
   | nmrPipe -fn EXT -xn 1024 -sw     \ 
   | nmrPipe -fn EM -lb 1 -c 0.5      \
   | nmrPipe -fn ZF -auto             \
   | nmrPipe -fn FT                   \
   | nmrPipe -fn PS -p0 100 -p1 0 -di \
     -out test.ft1 -ov

In some cases, an inverse-transform scheme might distort the last point in the time-domain result, which can cause problems if the scheme is used for Linear Prediction (LP). In these cases, we can use EXT with a negative point location to extract all but the last point in the inverse-processed data, for example:

   | nmrPipe  -fn HT  -auto          \
   | nmrPipe  -fn PS  -inv -hdr      \
   | nmrPipe  -fn FT  -inv           \
   | nmrPipe  -fn ZF  -inv           \
   | nmrPipe  -fn SP  -inv -hdr      \
   | nmrPipe  -fn EXT -xn -1 -sw     \
   | nmrPipe  -fn LP  -fb            \
   | nmrPipe  -fn SP  -hdr           \
   | nmrPipe  -fn ZF  -auto          \
   | nmrPipe  -fn FT                 \
   | nmrPipe  -fn PS  -hdr -di       \

Frank Delaglio, Ph.D.