Programs of the NMRPipe System

This particular reference page lists the programs of the NMRPipe system. Many are intended to be invoked directly at the UNIX command line, such as the graphical interface nmrDraw. Others are used primarily in C-shell scripts, such as the program xyz2pipe, which is used in 3D and 4D processing schemes. Most of the commands are binary executable programs. A few of the commands however, are actually C-shell or NMRWish TCL scripts.

Like xyz2pipe, many of these programs are used frequently. Some programs options, however, may rarely be used, were added only for development purposes, or may be superseded by other facilities. In an attempt to indicate which programs and options are used most frequently, this reference list includes an instance count. In the current version of this reference list, the instance count is a rough estimate of how often NMRPipe's developer Frank Delaglio has used a particular program or option in recorded examples of both routine use and research and development of the software.

Programs of NMRPipe

Name	Instances	Description	Common Arguments (Instances)
ACME	2	Graphical interface of the ACME system for extraction of COSY couplings; actually a script which invokes view2D.tcl with appropriate arguments.
DC	49	Stand-alone program for fitting or simulating dipolar couplings or protein backbone chemical shifts. See Also: NMRWish/DYNAMO TCL commands dynSimulate -dc and dynSimulate -cs.	`-pdb (28)` `-verb (28)` `-inD (25)` `-outD (25)` `-euler (8)` `-svd (5)` `-inCS (4)` `-outCS (4)` `-nofixed (3)`
IMATH	4	Print the results of a mathematical expression as an integer, for performing math in C-shell scripts. Actually a script which invokes the M macro interpreter.
M	8	Stand-alone version of the NMRPipe MAC macro language interpreter.	`-quit (8)` `-str (6)` `-var (3)`
MATH	20	Print the results of a mathematical expression as a floating point value, for performing math in C-shell scripts. Actually a script which invokes the M macro interpreter.
addNMR	50	Combine NMRPipe-format files by addition, subtraction, etc.	`-in1 (50)` `-in2 (50)` `-out (50)` `-sub (35)` `-add (7)` `-c1 (4)` `-c2 (4)` `-mul (4)` `-il (1)`
addNoise	7	Add Gaussian-random noise to NMRPipe-format data.
addTabVar	76	Add a variable (new column) to an NMRPipe-format table.	`-in (76)` `-var (76)` `-start (76)` `-col (4)`
bin2pipe	41	Generic utility to convert binary data to NMRPipe-format data.	`-xN (39)` `-xT (39)` `-xMODE (39)` `-xSW (39)` `-xOBS (39)` `-xLAB (39)` `-xCAR (37)` `-ndim (37)` `-in (35)`
bruk2pipe	212	Convert Bruker time-domain data to NMRPipe-format data; see also the bruker command for creating format conversion scripts.	`-xN (206)` `-xT (206)` `-xMODE (206)` `-xSW (206)` `-xOBS (206)` `-xCAR (206)` `-xLAB (206)` `-ndim (206)` `-aq2D (193)`
bruker	212	Graphical interface for Bruker spectrometer format conversion; actually a script which invokes conv.tcl to produce a bruk2pipe conversion script.
byteAdjust	9	Manipulate binary data for format conversion, such as integer-to-float conversion.	`-in (9)` `-iws (5)` `-ows (5)` `-out (5)` `-is (4)` `-bo (4)` `-last (3)` `-s2f (2)` `-d2f (2)`
byteSwap	1	Byte-swap binary data for format conversion.
clustTab	10	Identify clusters (overlapping groups) of objects based on their coordinates in an NMRPipe-format table. OBSOLETE: replaced by clustTab.tcl.	`-in (10)` `-out (10)` `-x (10)` `-dist (10)`
delta	2	Graphical interface for JEOL Delta spectrometer format conversion; actually a script which invokes conv.tcl to produce a delta2pipe conversion script.
delta2pipe	2	Convert JEOL Delta time-domain data to NMRPipe-format data; see also the delta command for creating format conversion scripts.	`-in (2)` `-out (2)`
extract2D	1	Extract a smaller 2D region from an NMRPipe-format 2D plane. OBSOLETE: replaced by stand-alone command readROI.
flagLoc	1	Utility for extracting command-line arguments from a C-shell script; returns the location of a flag on the command line.
getArgD	3	Utility for extracting command-line arguments from a C-shell script; sets the value of a variable according to a flag on the command line.	`-pdb (1)` `-r1 (1)` `-rN (1)`
getCols	4	Extract one or more columns from a text table. See also getTabCol.tcl and getTabInfo.tcl.	`- (1)`
getListArgD	1	Utility for extracting command-line arguments from a C-shell script; extracts a list of values associated with a flag on the command line.
getParm	1	Stand-alone program to extract parameters such as size and spectral width from NMRPipe-format data, commonly used to make spectral parameters available to C-shell scripts.
imClassify	1	Image analysis utility; creates a single binarized image according to values in an image series.
interp2D	1	Increase the size of an NMRPipe-format all-real spectrum using Fourier interpolation.
killShell	1	Utility to kill a group of UNIX processes associated with the given program name.
lst	1	Utility for listing or removing files according to their age.
modelXY	233	Stand-alone program for fitting and monte carlo error analysis of X/Y data pairs, using a function specified via the NMRPipe MAC macro language. See Also: the NMRWish TCL command of the same name, modelXY	`-macro (232)` `-gc (232)` `-p (230)` `-tol (230)` `-cf (227)` `-noise (225)` `-x (224)` `-y (224)` `-id (214)`
mstat	4	Print summary statistics (such as average and standard deviation) of a column in a text table.
nlinLS	47	General purpose multidimensional lineshape fitting of NMRPipe-format data. Usually invoked via autoFit.tcl.	`-in (47)` `-out (47)` `-maxf (47)` `-iter (47)` `-noise (47)` `-mod (47)` `-norm (46)` `-w (44)` `-data (25)`
nmr2Mask	1	Create a threshold-based binary mask from an NMRPipe-format all-real spectrum, with optional labeling of contiguous regions in the result.
nmrCsh	1	Utility used to launch NMRPipe parallel processing scripts on a single multi-CPU computer. See also: nmrShell, waitFor.
nmrDraw	334	Interactive interface for displaying NMRPipe-format spectral data, with facilities for processing, phasing, and peak detection. NOTE: nmrDraw (with upper-case D) is a script which runs the program nmrdraw with an appropriate collection of arguments; the nmrdraw program is generally NOT invoked directly.
nmrPipe	9768	Spectral processing of NMRPipe-format spectral data stream. Generally NOT invoked directly, but instead used in a UNIX pipeline via a C-shell script.	`-fn (9201)` `-di (1329)` `-verb (993)` `-out (691)` `-in (639)` `-ov (631)` `-noWr (86)` `-noRd (77)` `-inPlace (62)`
nmrPrintf	8	Command-line utility for formatted printing in the style of the C-programming language, often used in C-shell scripts to generate NMRPipe-style data file names.	`-stderr (8)` `-verb (2)`
nmrRecon	11	Reconstruct NMRPipe-format data from vector decomposition results, for example from program pcaNMR.	`-score (11)` `-load (11)` `-out (11)` `-ndim (7)`
nmrShell	1	Utility for network-based parallel processing with NMRPipe. NOTE: use simpler script nmrCsh For processing on a multi-CPU computer. See also: program waitFor
nmrTerm	1	Utility script for creating a terminal window; usually not invoked directly, but instead used by other NMRPipe scripts to run programs in the background.
nmrWish	420	NMRPipe's customized version of the TCL/TK interpreter wish, augmented with over 200 commands for manipulation of spectral and structural data. NOTE: not usually invoked directly, but instead used via a TCL script with the .tcl extension.
nocr	1	Utility for removing carriage-return characters so that Windows-format text files can be used with UNIX commands and NMRPipe.
pcaNMR	17	Principal Component Analysis for vector decomposition of NMRPipe-format data.	`-nc (17)` `-in (17)` `-load (17)` `-pca (9)` `-score (8)` `-noavg (8)` `-nomask (8)` `-noverb (7)` `-noise (1)`
pcaTab	1	Principal Component Analysis of data in an NMRPipe-format table.
pipe2ft	1	Convert NMRPipe-format data to the FTNMR format.
pipe2spiff	3	Convert NMRPipe-format data to the SPIFF image data format.	`-out (3)` `-verb (3)` `-ov (3)` `-in (1)`
pipe2xyz	465	Write the results of a 3D or 4D NMRPipe-format stream as an NMRPipe-format file series. Also used to write NMRPipe-format 1D-4D data stream as an NMRView-format file (See One Moon Scientific for more information about Bruce Johnson's NMRView)	`-out (464)` `-z (149)` `-x (135)` `-y (134)` `-ov (113)` `-inPlace (82)` `-verb (41)` `-to (20)` `-a (15)`
plotXY	1	Crude X/Y text plot of two columns from a text table.
readROI	16	Utility for extracting and saving a region-of-interest (ROI) from NMRPipe format spectral data. Actually a TCL script which invokes the NMRWish Built-In Function of the same name, readROI.	`-in (16)` `-x (16)` `-ndim (14)` `-dy (11)` `-silent (10)` `-out (6)` `-real (5)` `-imag (5)` `-y (5)`
scale2D	31	Extract and print the minimum and maximum intensity values in an NMRPipe-format data file.
seriesTab	17	Extract maximum intensities or summations for peak regions in an NMRPipe-format 2D spectral series, using an NMRPipe-format 2D peak table as input.	`-in (17)` `-list (17)` `-out (17)` `-dx (17)` `-dy (17)` `-verb (17)` `-max (15)` `-xzf (13)` `-yzf (13)`
setfdata	1	Set the value of a location in the header of an NMRPipe-format data file. See Also: sethdr.
sethdr	35	Set the value of a named parameter in the header of an NMRPipe-format data file. See Also: NMRPipe program getparm.	`-ndim (14)` `-tau (11)` `-zN (11)` `-zT (10)` `-zMODE (10)` `-zFT (10)` `-zSW (10)` `-zOBS (10)` `-zCAR (10)`
showApod	1	Estimate the noise level in an NMRPipe-format spectrum, and back-calculate the time-domain noise level according to the window functions (apodization) that were applied during processing. See Also: NMRPipe Processing Function MEM (Maximum Entropy Reconstruction).
showfdata	1	List the values in each location of the header in an NMRPipe-format data file. See Also: NMRPipe programs getParm, setfdata, and showhdr.
showhdr	7	Summarize the parameters in the header of an NMRPipe-format data file.	`-verb (4)`
simSpecND	30	Add simulated multidimensional signals to an existing NMRPipe-format all-real spectrum, given an NMRPipe-format peak table as input.	`-in (30)` `-mod (30)` `-w (30)` `-data (22)` `-apod (19)` `-list (8)`
simTD	31	Create simulated NMRPipe-format 2D time-domain data. OBSOLETE: replaced by simTimeND.	`-xt (30)` `-yt (30)` `-off (22)` `-in (8)` `-out (8)` `-xf (6)` `-yf (6)` `-rms (5)` `-ov (4)`
simTimeND	11	Create simulated NMRPipe-format multidimensional time-domain data, given an NMRPipe-format peak table as input.	`-in (11)` `-ndim (11)` `-aq2D (11)` `-xN (9)` `-yN (9)` `-xT (9)` `-yT (9)` `-xMODE (9)` `-yMODE (9)`
sortTab	1	Sort the lines in an NMRPipe-format table.
tkrm	1	Utility to list programs which are using X11 graphics as a means of inter-process communication, in the style of the TCL/TK send command; also used to remove obsolete entries in the list of such programs.
var2pipe	63	Convert Varian-format time-domain data to NMRPipe-format data.	`-xN (60)` `-xT (60)` `-xMODE (60)` `-xSW (60)` `-xOBS (60)` `-xCAR (60)` `-xLAB (60)` `-ndim (60)` `-in (59)`
varAdjust	1	Strips internal parameter information between vectors in Varian-format time-domain data. OBSOLETE. See: varAdjust.tcl
varian	63	Graphical interface for Varian spectrometer format conversion; actually a script which invokes conv.tcl to produce a var2pipe conversion script.
waitFor	39	Synchronize NMRPipe parallel processing schemes. See Also: nmrShell and nmrCsh.	`-par (39)` `-ext (39)` `-cpu (21)` `-init (18)` `-verb (6)`
xNotify	6	Utility to display a message in a pop-up window.
xyz2pipe	443	Read a 3D or 4D NMRPipe-format input, to create a stream for processing via the nmrPipe program.	`-in (442)` `-verb (355)` `-z (188)` `-x (178)` `-par (38)` `-cpu (34)` `-y (26)` `-a (18)` `-ri2c (5)`
zero2D	1	Set the all intensities of an NMRPipe-format file to zero; often used when creating simulated spectral data with simSpecND.

Frank Delaglio, Ph.D.