NMRPipe Processing Functions
JMOD: Exponentially Damped J-Modulation Profile.
JMOD is a window function which applies an exponentially damped sinusoid modulation to the given data. The purpose of the JMOD window is to approximate or reproduce a coupling-induced splitting. One use of this is to specify a deconvolution to be applied by a function such as MEM. The JMOD exponential term is specified as a Lorentzian line broadening in Hz (parameter lb). Likewise, the modulation frequency is expressed as a splitting in Hz (parameter jHz). There is an adjustable phase offset for the modulation (parameter off), making it possible to choose between cosine forms (in-phase modulation) and sine forms (anti-phase modulation).
In the following formula for JMOD,
tSize is the number of
time-domain points, which defines the length of the window
function; JMOD[i] is the window function from
i = 0 (first
i = tSize - 1 (last point); and
is the sweep width in Hz.
JMOD[i] = exp( -e )*sin( PI*off + PI*(end - off)*i/(tSize-1) )where
e = PI*i*lb/sw end = off + jHz*(tSize - 1)/sw
In addition to function-specific options, the JMOD window function provides the following features common to all NMRPipe window functions:
(Q1) Specifies the offset of the sinusoid modulation in units of pi radians. Usual values are 0.0 (for a sine modulation) and 0.5 (for a cosine modulation.
(Q2) Specifies the modulation frequency to apply in terms of a corresponding line splitting in Hz.
(Q3) Specifies the exponential to apply in terms of a line width in Hz. The default value is 0.0, which means no exponential term will be applied, and the window will be an undamped sinusoid.
Sets Q1 to 0.5, to provide cosine modulation.
Sets Q1 to 0.0, to provide sine modulation, which is the default.
GENERIC WINDOW OPTIONS
Specifies the number of points in the window function. The default value is the valid time-domain size recorded in the data header.
Specifies the starting point of the window function. The default value is 1, which means the window function starts at the first point of the FID. This option is intended for creation of composite windows by application of different functions to different regions of the FID.
Specifies the scaling applied to the first point of the FID, which influences the zero-order offset in the corresponding spectrum. The default value is 1.0, which means no first point adjustment is applied. A value of 0.5 is usually appropriate in cases where no substantial first-order phase correction will be applied.
This flag influences the values used "outside" the window function, in cases where the window size is smaller than the actual number of data points. By default, data values outside the window region are multiplied by zero when the window is applied. However if the
flag is used, data values outside the window region
will be multiplied by 1.0 when the window is applied.
This flag is intended to assist creation of composite
windows by application of different functions to different
regions of the FID.
When this flag is used, default window parameters (Q1, Q2, and Q3) will be extracted from the data header, along with the first point scaling. This requires that all of these parameters have already been recorded, for instance during previous processing or format conversion (see EXAMPLES below). Additional command-line can be used to override values restored from the header. The window parameters stored in the data header can be viewed using the showhdr program, for example:
showhdr -verb test.ft2
When this flag is used, the inverse (1/window) of the selected window and first point scale will be applied. This option is intended for removing a previously-applied window in inverse processing schemes. This option should generally only be used on window functions which have no values close or equal to zero. In cases where the window does have a zero value, the inverse window is also given as zero.
The following script introduces a 90Hz splitting to the 15N dimension of a 2D HN/N spectrum:
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 194 -p1 0.0 -di \ | nmrPipe -fn EXT -x1 10.5ppm -xn 6.5ppm -sw -verb \ | nmrPipe -fn TP \ | nmrPipe -fn JMOD -j 90 -cos \ | nmrPipe -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5 \ | nmrPipe -fn ZF -auto \ | nmrPipe -fn PS -p0 0 -p1 0 -di \ | nmrPipe -fn TP \ | nmrPipe -fn POLY -auto \ -verb -ov -out test.ft2
The following example includes Maximum Entropy Method (MEM) used to remove the simulated 90 Hz splitting which is applied in the first processing pipeline.
nmrPipe -in test.fid \ | nmrPipe -fn SOL \ | nmrPipe -fn ZF -zf 2 -auto \ | nmrPipe -fn FT \ | nmrPipe -fn PS -p0 194 -p1 0.0 -di \ | nmrPipe -fn EXT -x1 10.5ppm -xn 6.5ppm -sw -verb \ | nmrPipe -fn TP \ | nmrPipe -fn JMOD -j 90 -cos \ -out jmod.ft1 -verb -ov nmrPipe -in jmod.ft1 \ | nmrPipe -fn ZF -zf 2 \ | nmrPipe -fn FT -di \ | nmrPipe -fn TP \ | nmrPipe -fn MEM -ndim 2 -x0 0.0 -tScale 0.0 -sigma 60 -report 2 \ -xconv EM -xcQ1 10.0 \ -yconv JMOD -ycQ1 0.5 -ycQ2 90 -ycQ3 11.0 \ -out mem.ft2 -ov
JMOD and the other nmrPipe window functions use the recorded time-domain size (NDAPOD) to establish their default length.
-hdr flag is used, default window parameters are
extracted from header values NDAPODCODE, NDAPODQ1, NDAPODQ2,
NDAPODQ3, and NDC1.
The header values NDAPODCODE, NDAPODQ1, NDAPODQ2, NDAPODQ3, and NDC1 are updated according to the values applied during processing.