NMR Science - The Big NMRPipe Reference Page

Introduction

The NMRPipe system consists of a collection of programs and scripts for manipulating spectral data and molecular structures. Some scripts are written for the UNIX C-Shell interpreter, while others are written in the TCL scripting language. In particular, spectral processing is performed via C-shell pipeline scripts, using a series of nmrPipe processing functions. Applications written as TCL scripts are executed via nmrWish, our customized version of the "wish" interpreter. TCL scripts can make use of built-in functions that have been added to the interpreter. TCL scripts can also make use of procedures in the NMRPipe TCL/TK library. These are functions written in TCL that provide useful utilities for construction of other scripts.

Last Updated Feb 15, 2016

NMRPipe Big Reference Page

This reference page lists the following:

The programs and commands of the NMRPipe system, for example "nmrDraw", our graphical interface for spectral viewing. In most cases, the commands are binary executable programs, while in some cases, the commands are actually C-shell or NMRWish TCL scripts.

The specific processing functions that can be used in an nmrPipe processing pipeline (via nmrPipe -fn ...), for example "FT", the Fourier Transform function.

The application scripts which are part of the NMRPipe distribution, for example the "scroll.tcl" graphical application for displaying strip plots on the screen. These will generally end in ".com" (C-Shell script) or ".tcl" (NMRWish TCL/TK script).

The Built-In functions which have been added to the "nmrWish" TCL/TK interpreter, for example the "gdbRead" command for reading an NMRPipe-format table. These functions are only used within NMRWish TCL/TK scripts.

The TCL/TK script library functions which are provided with the NMRPipe installation. These scripts can be invoked from inside other TCL scripts to perform generally-useful tasks, as for example the "getArgD" function for extracting the value of a command-line option.

Many of these programs and scripts are used frequently in typical sessions with the software. Some facilities, however, may rarely be used, were added only for development purposes, or may be superseded by more recent additions to the software. In an attempt to indicate which commands and options are used most frequently, the reference list includes an instance count. In the current version of this Reference List, the instance count tallies how often NMRPipe's developer Frank Delaglio has used a command or option in a script during both routine use and research and development of the software. Note that this scheme will under-estimate the importance of interactive commands like "nmrDraw", which are used often, but seldom included in another script.

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.

NMRPipe Processing Functions

Function	Instances	Description	Common Arguments (Instances)
ADD	0	Add a Constant
APOD	11	Apply the Selected Window (Apodization)	`-inv (7)` `-hdr (7)` `-qName (4)` `-q1 (4)` `-q2 (4)` `-q3 (4)`
BASE	9	Linear Baseline Corrections	`-first (8)` `-last (8)` `-nw (8)` `-nl (6)`
CBF	20	Subtract Constant Baseline
COADD	31	Linear Combination of Data Vectors	`-cList (30)` `-axis (27)` `-time (25)`
CS	48	Circular Shift	`-rs (37)` `-sw (37)` `-neg (27)` `-ls (10)` `-1ppm (5)` `-inv (1)`
DX	0	Derivative
EM	35	Exponential Multiply Window	`-lb (34)` `-c (18)`
EXT	487	Extract Region	`-sw (455)` `-xn (317)` `-x1 (306)` `-left (157)` `-yn (7)` `-y1 (6)`
FSH	2	Frequency Shift via Fourier Transform	`-ls (1)` `-sw (1)`
FT	1597	Complex Fourier Transform	`-inv (178)` `-auto (111)` `-neg (53)` `-alt (25)` `-bruk (17)` `-real (11)`
GM	54	Lorentz-to-Gauss Window	`-g1 (53)` `-g2 (53)` `-c (53)` `-g3 (5)`
GMB	0	Gaussian Window
HA	0	Hadamard Transform
HT	155	Reconstruct Imaginary Data Via Hilbert Transform	`-auto (90)` `-ps90-180 (4)`
IMG	5	Image Processing Functions	`-median (3)` `-dx (2)` `-dy (2)` `-kern (1)` `-min (1)` `-thresh (1)`
INTEG	0	Integral
JMOD	0	Damped J-Modulation
LP	198	Linear Prediction	`-ord (148)` `-fb (93)` `-pred (74)` `-xn (46)` `-ps0-0 (28)` `-ps90-180 (18)`
LS	0	Left Shift
MAC	187	M-language MACRO Processing	`-macro (186)` `-all (67)` `-var (25)` `-str (14)` `-reg (9)` `-dif (6)`
MC	29	Modulus (Magnitude) Calculation for Complex Data	`-p0 (4)` `-p1 (4)`
MED	2	Baseline Correction via Local Median	`-nw (1)`
MEM	50	ND Maximum Entropy Reconstruction	`-sigma (49)` `-report (46)` `-ndim (42)` `-alpha (21)` `-zero (18)` `-xconv (17)`
MIR	2	Form Mirror Image
ML	22	Maximum Likelihood Frequency Map	`-xfSize (12)` `-ndim (11)` `-yfSize (10)` `-xlw (8)` `-sign (7)` `-report (5)`
MULT	92	Multiply by a Constant	`-xn (69)` `-c (63)` `-hdr (24)` `-inv (6)` `-r (4)` `-i (2)`
NULL	7	Null Function; Leave Data Unchanged
POLY	169	Polynomial Time-Domain Solvent Subtraction	`-time (169)`
POLY	562	Polynomial Frequency-Domain Baseline Correction	`-auto (390)` `-ord (134)` `-xn (20)` `-x1 (20)` `-window (3)` `-nw (3)`
PS	1333	Phase Correction	`-p0 (1176)` `-p1 (1167)` `-hdr (150)` `-inv (89)` `-ls (2)` `-rs (2)`
QART	6	Scale Quad Artifacts	`-a (5)` `-f (5)`
QMIX	5	General Linear Combination of Data Vectors	`-ic (5)` `-oc (5)` `-cList (5)` `-time (5)` `-0,1 (1)`
REV	17	Reverse Data	`-sw (2)`
RFT	0	Real Fourier Transform
RS	22	Right Shift	`-rs (21)` `-sw (11)`
SAVE	0	Save Current 1D Data Vector
SET	43	Set Data to Constant	`-r (25)` `-c (15)` `-x1 (9)` `-xn (8)`
SHUF	15	Shuffle Data (Exchange Reals and Imaginaries, etc)	`-exlr (7)` `-ri2c (2)` `-bswap (2)` `-swap (1)` `-c2ri (1)` `-r2i (1)`
SIGN	11	Sign Manipulation (Negate, etc)	`-alt (7)` `-i (3)`
SMO	3	Smooth Data via Convolution Filter
SOL	208	Solvent Filter	`-head (16)` `-mir (16)` `-fl (2)`
SP	1357	Adjustable Sine Bell Window	`-off (1204)` `-end (1160)` `-pow (1148)` `-c (1143)` `-inv (117)` `-hdr (117)`
TM	0	Trapezoid Window
TP	892	2D Transpose XY->YX (YTP)	`-hyper (47)` `-nohdr (7)` `-auto (2)`
TRI	2	Triangle Window	`-loc (1)`
ZD	0	Zero Diagonal Region
ZF	1580	Zero Fill	`-auto (941)` `-size (284)` `-zf (169)` `-inv (122)` `-mid (11)` `-pad (3)`
ZTP	35	3D Transpose XYZ->ZYX

NMRPipe Scripts

Name	Instances	Description	Common Arguments (Instances)
addFC.tcl	0	Add or replace the FC force-constant value for selected atoms in table.
addPDBNoise.tcl	0	Add random values to coordinates in a PDB file; commonly used for validation and error estimation.
addTabNoise.tcl	0	Add random noise to selected values in an NMRPipe-format table; commonly used for validation and error estimation.
addTabVar.tcl	4	Add a variable (column) to an NMRPipe-format table.	`-in (4)` `-var (4)` `-after (4)` `-fmt (4)` `-val (4)`
adjShift.tcl	8	Add an offset adjustment to ppm values in a TALOS-format chemical shift table.	`-in (8)` `-out (8)` `-atom (8)` `-adj (8)`
adjTab.tcl	0	Adjust Data in Selected Table Lines, with Optional Sorting.
angles.tcl	0	List the backbone angles in one or more PDB files. Replaced by dynAngles.tcl.
apod.com	20	Create 1D apodization files used for 1D time-domain models. See also: autoFit.tcl
apod.tcl	0	Demo script for interactive display of an NMRPipe apodization window.
appendTab.tcl	0	Append two NMRPipe-format tables.
autoFit.tcl	17	General purpose lineshape fitting of 1D, 2D, 3D and pseudo-3D NMRPipe-format data.	`-specName (17)` `-inTab (14)` `-series (8)` `-simName (5)` `-outTab (3)` `-thresh (2)` `-difName (2)` `-dX (2)` `-modX (1)`
clustTab.tcl	0	Perform cluster analysis on an NMRPipe-format table.
cmpFDATA.tcl	0	Compare the header values of two NMRPipe-format data files.
cont.tcl	0	Utility to consolidate lines in PostScript contour plots produced with NMRPipe tools.
conv.tcl	0	Graphical interface for Spectrometer data format conversion; invoked by commands varian, bruker, and delta.
convEuler.tcl	0	Convert XYZ-format Euler angles to a different format, such as ZYZ.
cs2pk.tcl	0	Create a synthetic peak table from a chemical shift table for common triple resonance experiments such as CBCANH.
dc2xplor.tcl	0	Convert a DYNAMO format dipolar coupling table to XPLOR format.
dcConvert.tcl	7	Convert XPLOR format Dipolar Coupling Data to DYNAMO format.	`-in (7)` `-pdb (7)` `-seg (7)`
dcEnsemble.tcl	0	SVD Fit of Dipolar Couplings for an Ensemble of PDB Files.
dcEval.tcl	0	Summarize agreement with dipolar couplings and backbone chemical shifts for each residue in a PDB file.
dcNoise.tcl	0	Add random noise to values in an NMRPipe-format dipolar coupling table; used in validation and error estimation.
deco.tcl	5	Decompose an NMRPipe-format 1D spectrum as a linear combination of others.	`-in (4)` `-inList (4)`
diffTab.tcl	0	List X/Y differences between two assigned tables; used to extract coupling data from two related peak tables for IP/AP (in-phase/anti-phase) spectra.
dosyView.tcl	0	Crude utility to view 1D evolution curves from a 2D interferogram.
draw1D.tcl	0	Demo script for 1D drawing.
dyn2di.tcl	0	Create
dynAngles.tcl	0	Print or display backbone and sidechain angles from a PDB.
dynAvg.tcl	3	Compute an average molecular structure.	`-align (3)` `-r1 (3)` `-rN (3)` `-in (3)` `-out (3)`
dynBasicExt.tcl	0	General utility to perform a DYNAMO molecular structure annealing scheme; commonly used to generate extended structures as a starting point for other calculations.
dynCenter.tcl	6	Adjust coordinates of a PDB structure to center it at the origin.	`-in (6)` `-out (6)`
dynEval.tcl	0	Evaluate a PDB file's agreement with the collection of DYNAMO molecular structure restraints.
expDemo.tcl	0	Demo script for X/Y fitting of an exponential curve.
findPDBSurf.tcl	0	Estimate the solvent-accessible surface of a PDB structure.
fitTab.tcl	0	An example of general-purpose X/Y fitting of values from a table.
fixCS.tcl	0	Apply offset correction to values in a TALOS-format chemical shift table.
fixPDB.tcl	0	Adjust a PDB for use in TALOS/DYNAMO database applications, for example by adding hydrogen atoms if needed.
fragSA.tcl	0	Utility to refine fragments found in an NMR homology search (MFR, Molecular Fragment Replacement)
getTabCol.tcl	0	Extract a column from an NMRPipe-format table; used to access table data from within a C-shell script.
getTabInfo.tcl	0	Extract table information, such as number of entries (rows) from an NMRPipe-format table; used to access table data from within a C-shell script.
getTabRow.tcl	0	Extract a row from an NMRPipe-format table; used to access table data from within a C-shell script.
gif2roi.tcl	0	Convert a GIF format grayscale image to an NMRPipe region-of-interest (ROI).
gmcEdit.tcl	0	Graphical interface for specifying sequence data to create a DYNAMO structure calculation environment.
imageView.tcl	0	Graphical interface for viewing and multivariate analysis of an image series such as a chemical shift image (3D spectral image).
ipap.tcl	3	Graphical interface to assign peaks in an NMRPipe-format peak table based on existing amide assignments.	`-assName (2)` `-single (2)` `-inName (2)` `-specName (2)` `-jx (2)` `-jy (2)` `-inName1 (1)` `-inName2 (1)` `-specName1 (1)`
j2dyn.tcl	0	Convert a table of J-coupling values into DYNAMO-format molecular calculation restraints.
jConvert.tcl	4	Convert XPLOR format J-Coupling Data to DYNAMO format.	`-in (4)` `-pdb (4)` `-seg (3)`
mapPDB.tcl	2	Map a parameter onto the temperature column of a PDB file, as a crude visualization tool.	`-in (2)` `-tab (2)` `-out (2)` `-inVar (2)` `-noseg (2)` `-vMin (2)` `-vMax (2)` `-all (2)`
mask.tcl	0	Create a binarized mask from NMRPipe-format data.
mfr.tcl	77	Conduct an NMR Parameter Homology Search for structure analysis by Molecular Fragment Replacement (MFR).	`-out (61)` `-ref (31)` `-daRef (28)` `-drRef (28)` `-rms (23)` `-ramaT (23)` `-csT (23)` `-rxRef (22)` `-ryRef (22)`
mfr2dyn.tcl	2	Convert results of a Molecular Fragment Replacement (MFR) homology search into DYNAMO structural restraints.	`-mfr (2)` `-pdb (2)` `-maxRank (2)` `-seg (2)` `-dHi (2)` `-ac (2)`
mfr2euler.tcl	0	Estimate relative orientation between two dipolar coupling alignment tensors from NMR homology search results (MFR, Molecular Fragment Replacement)
mfr2init.tcl	10	Create a protein structure based on average phi and psi backbone angles from a Molecular Fragment Replacement (MFR) homology search.
mfr2surf.tcl	5	Create phi/psi distribution surfaces from Molecular Fragment Replacement (MFR) homology search results.
mfr2torsion.tcl	0	Extract backbone torsion restraints from NMR homology search results.
modelExp.tcl	9	Utility for fitting peak evolution curves to exponential functions. Replaced by fitXY.tcl
mstat.tcl	0	Apply TCL script statistics functions to data from an NMRPipe-format table.
name2torsion.tcl	0	Convert a text file of named torsions such as phi and psi into DYNAMO-format molecular calculation restraints.
nmrCube.tcl	0	Draw a simple cube display of a 3D spectrum.
noeConvert.tcl	10	Convert XPLOR format NOE distance data to DYNAMO format.	`-in (10)` `-pdb (10)` `-seg (9)` `-min (1)` `-max (1)`
nusSort.tcl	5	Utility for expanding and re-ordering Non-Uniformly Sampled (NUS) NMRPipe-format data.	`-in (5)` `-out (5)` `-prof (5)` `-sample (5)`
orientDC.tcl	3	Find the optimal orientation between two domains in a PDB file using dipolar couplings.	`-ref (3)` `-pdb (3)` `-exit (2)` `-dc (1)`
ov.tcl	16	Compute the coordinate alignment and overlay between related PDB molecular structures.	`-ref (16)` `-in (16)` `-r1 (7)` `-rN (7)` `-noverb (3)` `-norot (2)` `-hdr (2)`
pcaLP.com	5	Utility for 2D Linear Prediction using Principal Component Analysis decomposition.	`-inDir (5)` `-outDir (5)` `-ordX (5)` `-ordY (5)` `-nc (5)` `-thresh (5)` `-extra (5)` `-ps0-0 (2)` `-xLP (1)`
pdb2ac.tcl	17	Extract DYNAMO atomic coordinate restraints from a PDB file.	`-in (17)` `-seg (17)` `-fc (15)` `-dHi (8)` `-id (5)` `-center (4)` `-atom (3)` `-dx (3)` `-nohdr (3)`
pdb2dyn.tcl	0	Extract DYNAMO residue creation data from a residue in a PDB; used to help add new residue types for DYNAMO structure calculation.
pdb2gmc.tcl	15	Use sequence information in a PDB file to create a DYNAMO structure calculation environment.	`-in (15)` `-seg (15)` `-gmc (15)` `-nohelix (12)` `-out (11)` `-rasmol (7)` `-noext (2)` `-cont (1)` `-append (1)`
pdb2hms.tcl	0	Create data needed for DYNAMO ring-current chemical shift calculation.
pdb2torsion.tcl	6	Extract DYNAMO torsion restraints from a PDB file.	`-seg (6)` `-in (6)` `-ref (6)` `-dPhi (6)` `-pPsi (6)` `-nohdr (4)` `-id (4)` `-hdr (2)`
pdbSelect.tcl	2	Select DYNAMO PDB files based on energy values recorded in their header data; used to select lowest energy structures, etc.	`-n (2)` `-pdb (2)`
pdbTrans.tcl	0	Apply a rotation or translation to a PDB molecular structure.
peakHN.tcl	15	Utility for automated peak detection of a 2D amide HN-N spectrum or projection, used to generate coords for a strip display 3D spectra.	`-proj (15)` `-in (15)` `-out (15)` `-hi (15)`
pipe2tiff.tcl	0	Convert NMRPipe-format data to
pipe2txt.tcl	0	Convert NMRPipe-format data to ASCII text listing the intensity values at each point.
pix.tcl	0	Demo script for spectral reading and drawing.
pkFilter.tcl	0	Extract columns from an NMRPipe-format peak table; used to create a simplified table for direct manipulation and viewing.
plot1D2D.tcl	0	Example script for 2D hard-copy PostScript plot generation with 1D projections.
plot3d.tcl	0	Example script for PostScript plotting of 2D planes in an NMRPipe-format 3D spectrum.
plotTab.tcl	2	Display simple XY plot of two columns from an NMRPipe-format table.	`-in (2)` `-x (2)` `-y (2)` `-z (2)` `-select (2)` `-xMin (1)` `-xMax (1)` `-yMin (1)` `-yMax (1)`
proj2D.tcl	0	Create 2D projections from NMRPipe-format 3D-spectra.
proj3D.tcl	35	Form 2D projections from a 3D NMRPipe-format spectrum	`-in (34)` `-abs (24)`
rama.tcl	0	Graphical interface for TALOS.
randDel.tcl	2	Randomly delete entries in a table; used in cross-validation and error estimation.	`-in (2)` `-out (2)` `-del (2)` `-iseed (2)` `-noverb (2)` `-keep (1)`
renamePDB.tcl	0	Rename PDB atoms to conform with DYNAMO protocol, for example convert amide atom name H to HN.
resProbCS.tcl	0	Compute residue-type probability based on chemical shift.
resetLW.tcl	0	Adjust the linewidth values in an NMRPipe-format peak table, commonly to provide better starting values for lineshape fitting.
resetPhiPsi.tcl	6	Reset the backbone angles in a protein PDB structure, commonly to make an extended structure or helix.	`-in (6)` `-out (6)` `-pdb (3)` `-verb (3)` `-noall (3)`
rotDC.tcl	9	Add tensor information to a PDB file; crude method to visualize results from Dipolar Coupling analysis.	`-pdb (9)` `-in (9)` `-rx (8)` `-out (6)` `-ignore (5)` `-noaxis (5)` `-nohalo (5)` `-ry (4)` `-halo (4)`
rotPCS.tcl	0	Add tensor information to a PDB file; crude method to visualize results from Pseudo-Contact Shift analysis.
scale.tcl	5	Find the factor which minimizes the difference in the residual between two NMRPipe-format data files.	`-in1 (5)` `-in2 (5)` `-mask (5)` `-ndim (5)` `-window (5)` `-step (5)` `-out (5)` `-noverb (5)` `-def (5)`
scaleDI.tcl	0	Set or scale values in a dipolar coupling table.
scanCS.tcl	6	Create phi/psi surfaces showing regions most favored according to backbone chemical shifts.
scroll.tcl	78	General purpose strip viewing tools for one or more related NMRPipe-format 3D spectra.	`-in (78)` `-tab (78)` `-hi (76)` `-pair (68)` `-lab (13)` `-zw (9)` `-xVar (6)` `-yVar (6)` `-xName (4)`
scrollRama.tcl	9	Graphical interface for viewing ramachandran trajectories for one or more PDB files, or for fragment results from a Molecular Fragment Replacement (MFR) homology search.	`-pdb (9)` `-mfr (6)` `-pdbColor (6)` `-ref (6)` `-mfrColor (2)` `-r1 (1)` `-rN (1)`
selectTab.tcl	0	Utility for extracting lines from a table according to a given condition.
seq2gmc.tcl	13	Use sequence information from a table such as a TALOS chemical shift table to create a DYNAMO structure calculation environment.	`-in (13)` `-seg (13)` `-gmc (13)` `-rasmol (9)` `-out (3)` `-helix (3)`
series.com	11	Reset the headers of a 2D NMRPipe-format spectral series to create a Pseudo-3D result.
shift2tab.tcl	0	Convert PIPP-format assignments to NMRPipe-table format.
showCS.tcl	3	Display observed versus calculated chemical shifts.	`-in (3)` `-nograph (1)` `-noverb (1)`
showDC.tcl	8	Display observed versus calculated dipolar couplings.	`-in (8)` `-single (2)`
showEvolve.tcl	0	Graphical interface for displaying evolution curves, such as results from analysis of 2D relaxation series.
showSim1D.tcl	0	Graphical interface for displaying 1D lineshape fitting results.
showTab.tcl	0	NMRPipe-format Table Viewer.
sim1D.tcl	0	Utility for creating 1D synthetic data from lineshape fitting results.
simAB.tcl	0	Example of simultaneous fitting of two dipolar coupling tensors.
simCS.tcl	0	Utility for calculating backbone chemical shifts for a protein PDB.
simPCS.tcl	2	Utility for calculating backbone chemical shifts for a protein PDB.	`-in (2)` `-out (2)` `-noverb (2)` `-pdb (1)`
simple.tcl	0	Demo script illustrating spectral drawing.
splitPDB.tcl	0	Create individual PDB files from a PDB with multiple MODEL structures.
splitSeg.tcl	0	Create individual PDB files from a PDB with multiple SEGID structures.
ss.tcl	5	Analyze a PDB structure for secondary structure classification and hydrogen bonds.	`-dssp (5)` `-pdb (5)` `-verb (5)`
star2cs.tcl	0	Convert STAR format data to TALOS-format chemical shift table.
stripPlot.tcl	0	Create PostScript plots of strips from 3D NMRPipe-format spectra.
svdPoly.tcl	0	Polynomial fitting of X/Y data.
svdTab.tcl	0	Perform least-squares decomposition on data in an NMRPipe-table.
talos.tcl	0	TALOS - prediction of phi and psi protein backbone angles using chemical shifts.
talos2dyn.tcl	6	Convert TALOS protein backbone angle predictions to DYNAMO molecular structure calculation restraints.	`-in (6)` `-pdb (6)` `-seg (6)` `-id (3)`
talos2shift.tcl	0	Convert TALOS chemical shift table to format with multiple shifts per row.
talos2xplor.tcl	0	Convert TALOS backbone angle predictions to XPLOR-format restraints.
torsionConvert.tcl	6	Convert XPLOR-format torsions into DYNMAMO molecular structure calculation restraints.	`-in (6)` `-pdb (6)` `-seg (6)` `-id (1)` `-fc (1)`
txt2bin.tcl	0	Convert ASCII text values to binary data.
txt2pipe.tcl	0	Convert ASCII text values to NMRPipe-format data.
updateTab.tcl	0	Update the chemical shift positions in an NMRPipe-format peak table, based on the positions recorded in points.
varAdjust.tcl	0	Utility to adjust Varian-format fid data, to re-order interleaved data or to separate multiple experiments.
view2D.tcl	0	Graphical interface to view two or more 2D spectra in overlay mode.
vina.tcl	0	TALOS - prediction of phi and psi protein backbone angles using chemical shifts.

NMRWish Built-In TCL Functions

Name	Instances	Description	Common Arguments (Instances)
buildHdr	15	Create and set an NMRPipe-format data file header; often used to create synthetic data.	`-xN (15)` `-xT (15)` `-xMODE (15)` `-xSW (15)` `-xOBS (15)` `-xCAR (15)` `-xLAB (15)` `-ndim (15)` `-xFT (13)`
decoNMR	3	Matrix decomposition of NMRPipe-format data by nonlinear least-squares.	`-rdata (2)` `-fdata (2)` `-noise (2)` `-thresh (2)` `-verb (2)` `-step (2)` `-tol (2)` `-nc (2)` `-help (1)`
defineCell	219	Define a cell, which is a spectral drawing region on the screen or PostScript page.	`-x (219)` `-cell (219)` `-y (218)` `-win (138)` `-verb (47)` `-roiRef (8)` `-cellRef (4)`
drawBox	39	Draw a rectangular outline in the spectral graphics area of the screen or a PostScript page.	`-x (39)` `-y (39)` `-fg (39)` `-cell (11)` `-roi (3)`
drawLine	80	Draw a line in the spectral graphics area of the screen or a PostScript page.	`-x (80)` `-fg (79)` `-y (71)` `-cell (62)` `-roi (26)` `-roiRef (18)` `-thick (9)`
drawROI	285	Draw spectral data (a Region-of-Interest, or ROI) in a graphics area of the screen or a PostScript page.	`-roi (285)` `-cell (279)` `-bg (239)` `-hi (185)` `-color1 (108)` `-color2 (103)` `-fg (101)` `-axis (96)` `-plev (77)`
drawRec	179	Draw a filled rectangle in the spectral graphics area of the screen or a PostScript page.	`-x (179)` `-y (179)` `-fg (179)` `-cell (98)` `-noupdate (34)` `-roiRef (16)` `-roi (11)` `-win (6)` `-extendedColor (1)`
drawSettings	21	Adjust the parameters for drawing in the spectral graphics area of the screen or PostScript page.	`-reset (19)` `-extendedColor (2)`
drawText	125	Draw text in the spectral graphics area of the screen or a PostScript page.	`-x (125)` `-y (125)` `-text (125)` `-fg (106)` `-cell (102)` `-yOff (37)` `-bg (35)` `-center (24)` `-roiRef (21)`
dynAlign	64	Find the translation and rotation that minimizes the difference in coordinates between two related molecular structures.	`-aSrc (64)` `-refSrc (62)` `-r1 (59)` `-rN (59)` `-a1 (59)` `-atom (15)` `-apply (15)` `-verb (15)` `-max (4)`
dynCopy	0	Copy a DYNAMO object. Currently, only copies a PDB object.
dynCreate	0	Create a DYNAMO object.
dynDestroy	0	Destroy (de-allocate) DYNAMO object and the resources associated with it. Same as dynFree. Currently, only works for PDB, CS (Chemical Shift) and DC (Dipolar Coupling) objects.
dynDynamics	3	Take a dynamics step in a simulated annealing molecular structure calculation.	`-src (3)` `-timeStep (3)` `-tempControl (3)` `-temp (3)` `-init (1)`
dynEnergy	4	Evaluate the energy at a given step of a simulated annealing molecular structure calculation.	`-src (4)` `-bond (4)` `-dist (4)` `-angle (4)` `-improper (4)` `-torsion (4)` `-j (4)` `-dt (4)` `-ac (4)`
dynEuler	20	Find possible XYZ-format rotational angles associated with a given rotation matrix, or find the rotation angles that map one rotation onto another.
dynEval	9	Evaluate the energy of a given structure.	`-src (9)` `-dc (1)` `-j (1)` `-angle (1)` `-uangle (1)` `-improper (1)` `-torsion (1)` `-bond (1)` `-ac (1)`
dynFree	121	Same as dynDestroy	`-src (4)` `-cs (4)` `-pdb (1)` `-dc (1)`
dynGet	0	Gets a DYNAMO parameter.
dynGetAlpha	0	Get the alpha torsion angle CA(i-1) CA(i) CA(i+1) CA(i+2) for selected residues.
dynGetAngle	0	Gets the angle formed by the three specified atoms.
dynGetAtomInfo	0	Get the parameters associated with an atom, such as atom name, residue name, and coordinates.
dynGetChi	12	Get the Chi sidechain angle for selected residues.	`-src (12)` `-res (12)` `-all (11)` `-chi1 (1)`
dynGetCoord	17	Get the coordinates for selected atoms.	`-src (17)` `-atomEntry (17)` `-verb (10)` `-dyn (1)`
dynGetDist	19	Get the distance between two specified atoms.	`-src (19)` `-atomI (13)` `-atomJ (13)` `-contact (6)` `-verb (6)` `-dist (6)`
dynGetInfo	266	Get information associated with a DYNAMO object; commonly, used to extract the first and last residue ID in a molecular structure.	`-src (264)` `-res (65)` `-resName (60)` `-all (10)` `-extent (6)` `-segName (3)` `-limits (3)` `-seg (2)` `-atomName (2)`
dynGetKappa	0	Get the Kappa angle CA(i-2) CA(i) CA(i+2) of selected residues.
dynGetNAAngles	2	Get angles from a Nucleic Acid structure.	`-src (2)` `-res (2)`
dynGetOmega	12	Get the Omega torsion angle CA(i-1) C(i-1) N(i) CA(i) from selected residues.	`-src (12)` `-res (12)`
dynGetPDBStr	25	Create a text entry describing an atom in the form of a PDB ATOM line.	`-resID (21)` `-resName (21)` `-atomName (21)` `-chain (21)` `-x (21)` `-y (21)` `-z (21)` `-atomID (4)`
dynGetPhi	5	Get the protein backbone torsion angle phi C(i-1) N(i) CA(i) C(i) for selected residues.	`-src (5)` `-res (5)`
dynGetPhiPsi	111	Get the protein backbone torsion angle pair phi and psi for selected residues.	`-res (111)` `-src (111)` `-phi (1)` `-psi (1)`
dynGetPsi	5	Get the protein backbone torsion angle psi N(i) CA(i) C(i) N(i+1) for selected residues.	`-src (5)` `-res (5)`
dynGetTorsion	3	Get the torsion associated with the four named atoms.	`-src (3)` `-atomI (3)` `-atomJ (3)` `-atomK (3)` `-atomL (3)`
dynHomology	8	Compute a simple residue type homology score for two amino acid sequences of the same length.	`-refSrc (8)` `-aSrc (8)` `-r1 (8)` `-rN (8)` `-a1 (8)`
dynInit	300	Initialize the DYNAMO structure manipulation environment.	`-fast (106)` `-nowarn (43)` `-warn (6)`
dynRama	6	Compute a ramachandran statistic for the backbone angles of a protein or fragment.	`-refSrc (6)` `-aSrc (6)` `-a1 (6)` `-r1 (5)` `-rN (5)` `-s1 (1)` `-sN (1)`
dynRead	593	Read a table or molecular structure for the DYNAMO structure manipulation environment.	`-in (593)` `-pdb (372)` `-verb (191)` `-dc (110)` `-src (66)` `-r1 (65)` `-rN (65)` `-cs (58)` `-atomName (55)`
dynRestore	32	Restore molecular coordinates which were first saved by dynStore	`-src (2)`
dynRotate	37	Apply a 3D rotation to the given molecular structure.	`-rx (37)` `-ry (37)` `-rz (37)` `-src (34)` `-all (31)` `-verb (6)` `-center (3)` `-inv (2)`
dynSearch	20	Perform NMR Homology Search (Molecular Fragment Replacement)	`-search (16)` `-src (12)` `-pdbName (8)` `-r1 (6)` `-rN (6)` `-init (4)` `-cs (4)` `-homoW (4)` `-ramaW (4)`
dynSelect	54	Select atoms according to the specified conditions, such as by residue name, etc.	`-src (52)` `-res (21)` `-atom (19)` `-list (19)` `-atomName (16)` `-clear (12)` `-glob (7)` `-seg (6)` `-r1 (6)`
dynSet	0	Set a DYNAMO parameter, such as the temperature in a simulated annealing schedule.
dynSetAtomInfo	0	Set the information associated with an atom, such its coordinates.
dynSetAtomName	0	Set the atom name for selected atoms.
dynSetChain	26	Sets the chain name for selected atoms.	`-src (26)` `-chain (22)` `-id (4)`
dynSetChainMode	46	Allow PDB chain name to be ignored when selecting and identifying atoms.	`-ignore (46)`
dynSetChi	0	Set the protein sidechain angles for selected residues.
dynSetCoord	4	Set the coordinates of the given atom.	`-src (4)` `-atomEntry (4)` `-x (2)` `-y (2)` `-z (2)` `-charge (1)` `-occ (1)`
dynSetInfo	0	Set information associated with a DYNAMO object.
dynSetOmega	0	Set the omega angle CA(i-1) C(i-1) N(i) CA(i) for the selected residues.
dynSetPhiPsi	131	Set the protein backbone angles phi C(i-1) N(i) CA(i) C(i) and psi N(i) CA(i) C(i) N(i+1) for the selected residues.	`-src (131)` `-res (131)` `-phi (131)` `-psi (131)` `-store (99)`
dynSetResName	0	Set the residue name for selected atoms.
dynSetSeg	10	Set the segment name for selected atoms.	`-src (10)` `-seg (6)`
dynSetSegMode	47	Allow PDB segment name to be ignored when selecting and identifying atoms.	`-ignore (47)`
dynSetTempFactor	0	Set the temperature factor for a DYNAMO annealing scheme.
dynSetTemperature	0	Set the temperature for a stage in a DYNAMO annealing scheme.
dynSetTensor	43	Set the parameters associated with an alignment tensor, as used in dipolar coupling and pseudo-contact shift calculation.	`-dc (42)` `-da (32)` `-dr (32)` `-dadr (27)` `-auto (22)` `-rxRef (16)` `-ryRef (16)` `-rzRef (16)` `-rotref (15)`
dynSimulate	239	Calculate NMR parameters from structure, including backbone chemical shifts, dipolar couplings, and J-couplings.	`-src (239)` `-a1 (160)` `-s1 (140)` `-sN (140)` `-dc (129)` `-verb (72)` `-cs (56)` `-svd (48)` `-r1 (42)`
dynStore	0	Store a temporary copy of a PDB structure's coordinates.
dynSurface	19	Compute the solvent-accessible surface.	`-refSrc (14)` `-aSrc (14)` `-r1 (14)` `-rN (14)` `-a1 (14)` `-src (5)` `-r (2)` `-tol (2)` `-verb (1)`
dynTransform	7	Apply rotation and translation to a molecular structure.	`-src (4)` `-all (4)` `-center (3)` `-reset (2)` `-verb (2)` `-m (1)` `-apply (1)`
dynTranslate	15	Apply translation to a molecular structure.	`-src (15)` `-all (12)` `-center (8)` `-tx (7)` `-ty (5)` `-tz (5)` `-verb (2)`
dynWrite	274	Write the DYNAMO table or molecular structure.	`-out (273)` `-src (167)` `-pdb (161)` `-verb (106)` `-rem (83)` `-dc (47)` `-cs (33)` `-renumber (10)` `-j (9)`
fixHdr	0	Adjust an NMRPipe-format header to handle byte-swapping.
freeCell	0	Remove the definition of a spectral drawing area (cell) on the screen or PostScript page.
freeROI	0	Delete the spectral data region (ROI, region-of-interest).
gammaq	0	Calculate the Incomplete Gamma Function Value
gdbAddNote	40	Add a text entry, such as a comment line, to a GDB Database table.
gdbAppend	3	Append one GDB table after another; commonly, this will be done for two tables which have the same number of columns. See Also: gdbJoin	`-src (3)` `-dest (3)`
gdbCheck	2	Test the integrity of the GDB database.	`-verb (2)`
gdbCreate	279	Create a GDB database object; commonly used to add a variable (column) or entry (row) to a table.	`-name (122)` `-parent (116)` `-varType (87)` `-varFmt (87)`
gdbDelNote	2	Delete a given text entry in a GDB database table.
gdbDestroy	94	Delete GDB database object; commonly used to delete the contents of a table when it is no longer needed.	`-verb (1)`
gdbFindByName	104	Find a GDB object by its name; commonly used to find a particular variable (column) in a given table.
gdbFirst	176	Find the first entry (row) in a table.
gdbFree	79	Same as gdbDestroy.
gdbGet	2684	Extract the value associated with a database cell, which is a particular value in a table, specified by its entry (row) and variable (column).
gdbGetInfo	543	Get information about an object in the GDB database; commonly used to get a list of entries (rows) in a table.	`-parms (542)` `-params (1)`
gdbInit	157	Initialize the GDB database engine; usually not needed, because this step is performed automatically the first time that a table is read by the gdbRead command.
gdbJoin	0	Join two tables along the rows; commonly, this will be done for two tables which have the same number of rows.
gdbLast	6	Find the last entry (row) in a GDB database table.
gdbNext	237	Find the next entry in a GDB database.
gdbPrev	9	Find the previous entry in a GDB database.
gdbRead	643	Read a NMRPipe-format database table or PDB file into the GDB database engine.	`-in (643)` `-name (129)` `-pdb (70)` `-verb (53)` `- (3)` `-hetatm (3)`
gdbReverse	0	Reverse the order of GDB objects, such as entries (rows) in a table.
gdbSelect	322	Perform a database Query, i.e., select entries from a GDB table according to one or more conditions.	`-from (322)` `-cond (322)` `-inPlace (67)` `-M (61)` `-new (23)` `-tcl (13)` `-mSQL (5)` `-vars (1)`
gdbSet	408	Set the value associated with a database cell, which is a particular value in a table, specified by its entry (row) and variable (column).
gdbSetInfo	0	Set the information associated with a GDB database object.
gdbSetVal	8	Same as gdbSet
gdbSort	7	Sort the data in a GDB database table according to a given column (variable). OBSOLETE: replaced by the more flexible function gdbSortTab.
gdbSortTab	5	Sort the data in a GDB database table according to a given column (variable).	`-down (1)` `-abs (1)`
gdbSwap	0	Swap the order of two objects in a GDB database, such as two entries (rows) in a table.
gdbTest	0	Test whether a GDB cell (value at a given row and column) has data or is empty.
gdbWrite	116	Write the GDB database table.	`-noverb (21)` `-pdb (16)` `-verb (1)`
geco	0	Genetic Algorithm for Combinatorial Optimization.
getBinary	0	Get the value at a pointer location in a binary array as a hex number.
getCellInfo	37	Get the graphics coordinates and parameters associated with a cell, which is a spectral drawing region on the screen or a PostScript page.	`-cell (35)` `-win (12)` `-x (5)` `-y (5)` `-roi (3)`
getParm	217	Get the named numerical parameter, such as size or spectral width, from an NMRPipe-format data header in a binary array. See also: TCL script function rdFDATA, nmrWish commands buildHdr and sysMemory.
getParmStr	90	Get the named text parameter, such as axis label, from an NMRPipe-format data header in a binary array. See also: nmrWish functions getParm and sysMemory.
getPtrStr	4	Get the packed text at a pointer location in a binary array.
getPtrVal	248	Get the numerical value at a pointer location in a binary array.
getROIInfo	333	Get information associated with a an ROI (region of interest), specifically binary data pointers to the spectral data and header, and the sizes of each dimension of the ROI. See also: nmrWish functions readROI, getParm, getPtrVal, and the nmrWish binary vector functions .	`-roi (333)`
incrPtr	62	Return a new nmrWish binary data pointer after incrementing the location that it references.
incrPtrVar	0	Adjust variable whose value is an nmrWish binary data pointer.
modelXY	18	Non-linear least squares fitting of X/Y data pairs with monte carlo error analysis, according to a fitting function specified in TCL.	`-y (18)` `-p (18)` `-x (14)` `-macro (14)` `-gc (14)` `-noverb (11)` `-noise (10)` `-tol (8)` `-res (8)`
newScreen	58	Clear the graphics screen. See also: drawROI.	`-win (22)`
nmrExec	0	Execute an NMRPipe processing function on nmrWish binary data. See also: nmrInit, nmrFree.
nmrFree	0	De-allocate information for using an NMRPipe processing function within nmrWish. See also: nmrInit and nmrExec.
nmrInit	0	Initialize information and resources so that NMRPipe vector processing functions can be applied to nmrWish binary data.
pcaNMR	0	Principal Component Analysis matrix decomposition on spectral data in a region of interest (ROI). See also: readROI, reconNMR.
pdbAngle	14	Get the angle formed by three atoms in a PDB file, using nmrWish GDB database entries.
pdbCoords	0	Get the coordinates and other information of associated with an atom in a PDB file, using nmrWish GDB database entries.
pdbDist	11	Get the distance between atoms in a PDB file, using nmrWish GDB database entries.
pix2spec	74	Convert a pixel location in a spectral drawing area into spectral units such as PPM. See also: defineCell, readROI, drawROI	`-cell (74)` `-units (74)` `-roi (72)` `-x (40)` `-y (36)` `-win (17)` `-roiRef (2)`
pkFindROI	82	Perform peak detection on the given spectral region of interest (ROI). See also: readROI. NOTE: this command over-writes the given ROI spectral data.	`-roi (81)` `-sigma (81)` `-pChi (81)` `-plus (81)` `-minus (81)` `-dx (81)` `-idx (81)` `-out (81)` `-tol (80)`
pkLabelROI	0	Perform component labeling on the given spectral region of interest (ROI). See also: readROI, pkFindROI.
plotClose	59	Close the current PostScript plot file. See also: plotOpen, defineCell, drawROI.
plotOpen	40	Open a PostScript plot file for creating hard-copy spectral graphics. See also: defineCell, readROI, drawROI	`-color (36)` `-landscape (34)` `-paper (17)` `-plotName (13)` `-tray (4)` `-portrait (3)` `-c1Width (2)` `-c1Height (2)` `-lwPlus (1)`
plotSend	0	Send a finished PostScript plot file to the printer.
plotSettings	2	Adjust the settings for PostScript plot generation.	`-reset (2)`
plotWrite	6	Write text into the current PostScript plot file.
pnt2spec	96	Convert a point location to a location in spectral units such as PPM, given an NMRPipe-format header as nmrWish binary data.
pnt2specW	4	Convert a width specified in points to a width specified in spectral units such as Hz, given an NMRPipe-format header as nmrWish binary data.
rand	81	Return a uniformly distributed or gaussian random number. See also: srand.	`-gauss (8)`
readROI	676	Read a region of interest (ROI) from NMRPipe-format data.	`-roi (675)` `-in (654)` `-ndim (525)` `-x (366)` `-y (290)` `-verb (103)` `-dy (90)` `-z (62)` `-dx (54)`
reconNMR	4	Reconstruct NMRPipe-format data from decomposition results produced by pcaNMR.	`-x (4)` `-y (4)` `-z (4)` `-c (2)`
setBinary	0	Set the hex value at a pointer location in a binary array.
setCellKey	0	Associate information with a spectral drawing area (cell).
setParm	221	Set the named numerical parameter, such as size or spectral width, in an NMRPipe-format data header in a binary array. See also: TCL script function rdFDATA, nmrWish commands buildHdr and sysMemory.
setParmStr	2	Set the named text parameter, such as size or spectral width, in an NMRPipe-format data header in a binary array.
setPtrStr	0	Set the packed text value at a pointer location in a binary array.
setPtrVal	134	Set the numerical value at a pointer location in a binary array.
setROIKey	0	Associate data with a spectral region of interest (ROI). See also: readROI, drawROI.
spec2pix	215	Convert a location in spectral units such as PPM to a pixel location in a spectral drawing area and a particular region-of-interest (ROI). See also: defineCell, readROI, drawROI.	`-cell (215)` `-roi (123)` `-x (109)` `-y (106)` `-win (38)` `-nofold (7)` `-roiRef (4)`
spec2pnt	17	Convert a location in spectral units such as PPM to a point location in a particular region-of-interest (ROI). See also: readROI.
spec2pntW	18	Convert a width spectral units such as Hz to a width in points for a particular region-of-interest (ROI). See also: readROI.
srand	108	Set the random number seed for the rand random number generation function.
strcasecmp	1239	Compare two strings, case-insensitive.
strcmp	288	Compare two strings, case-sensitive.
svdLinSol	15	Use Singular Value Decomposition to solve a linear least squares matrix problem.	`-x (15)` `-y (15)`
swapHdr	0	Perform byte-swap on the NMRPipe-format header in an nmrWish binary data array.
sysByteSwap	0	Perform byte-swap on data in an nmrWish binary data array.
sysClose	28	Close a binary data file previously opened with sysOpen.
sysFree	46	De-allocate a binary data array previously allocated by sysMalloc.
sysMalloc	79	Allocate an nmrWish binary data array, return a pointer which references the array.
sysOpen	37	Open a binary data file or pipeline command for reading or writing. See also: sysRead, sysWrite, sysClose.
sysRead	19	Read binary data into an nmrWish binary data array, with automatic byte-swapping. Non-blocking form (returns immediately if no data is available). See also: sysOpen, sysReadB.
sysReadB	0	Read data into an nmrWish binary data array, with automatic byte swapping. Blocking version (stops until data is available, used for reading pipelines rather then files). See also: sysOpen, sysReadB.
sysReadBNS	0	Same as sysReadB, but without automatic byte swapping.
sysReadNS	0	Same as sysRead, but without automatic byte swapping.
sysSeek	0	Move to a particular location in a binary data for reading or writing. See also: sysOpen, sysRead, sysWrite.
sysTime	29	Return the current time in seconds and milliseconds.
sysWrite	37	Write binary data from an nmrWish binary data array, with automatic byte-swapping. Non-blocking form (returns immediately if no data is available). See also: sysOpen, sysWriteB.
sysWriteB	0	Write binary data from an nmrWish binary data array, with automatic byte-swapping. Blocking form (stops until data can be written, used for writing to pipelines rather then files). See also: sysOpen, sysWriteB.
system	10	Execute a UNIX command.
testHdr	0	Test the NMRPipe-format file header data in an nmrWish binary array, to determine if the data needs to be byte-swapped. See also: rdFDATA, fixHdr, sysOpen, sysRead.
updateHdr	5	Update the PPM calibration information for the NMRPipe-format header an nmrWish binary array. See also: rdFDATA, setParm.
vACos	0	Apply function to nmrWish floating-point binary data: arc cosine.
vASin	0	Apply function to nmrWish floating-point binary data: arc sine.
vAbs	9	Apply function to nmrWish floating-point binary data: absolute value.
vAbsCor	0	Perform an optical absorbance correction to floating-point binary data.
vAvg	0	Compute the average of values in floating-point binary data.
vBinarize	2	Binarize (set to 1 or 0) values in floating-point binary data according to their range.
vByteSwap	2	Apply byte-swap to nmrWish binary data.
vCos	0	Apply function to nmrWish floating-point binary data: cosine.
vEstNoise	29	Estimate the noise level of spectral data in an in an nmrWish floating-point binary data array. See also: sysRead, readROI.
vExp	0	Apply function to nmrWish floating-point binary data: exponential.
vInterp	0	Perform linear interpolation on floating-point binary data.
vLinSol	5	Perform linear least squares computation on floating-point binary data.	`-xPtr (5)` `-yPtr (5)` `-aPtr (5)` `-ePtr (5)` `-eCount (5)` `-vCount (5)` `-cCount (5)` `-eJump (5)` `-vJump (5)`
vLog	0	Apply function to nmrWish floating-point binary data: logarithm.
vMax	60	Find the maximum value in an nmrWish floating-point binary data array.
vMaxAbs	0	Find the maximum absolute value in an nmrWish floating-point binary data array.
vMaxLoc	2	Find the point location of the maximum value in an nmrWish floating-point binary data array.
vMedian	0	Find the median value in an nmrWish floating-point binary data array.
vMin	44	Find the minimum value in an nmrWish floating-point binary data array.
vMinAbs	0	Find the minimum absolute value in an nmrWish floating-point binary data array.
vMinLoc	0	Find the point location of the minimum value in an nmrWish floating-point binary data array.
vNeg	0	Apply function to nmrWish floating-point binary data: negate.
vPDF	0	Utility for Probability Surface generation.
vPDFCoords	2	Utility for Probability Surface generation.
vRMS	13	Find the root mean square (RMS) of values in an nmrWish floating-point binary data array.
vResize	2	Resize a 1D, 2D or 3D data matrix in an nmrWish floating point data array using Fourier interpolation.	`-src (2)` `-ndim (2)` `-xSize (2)` `-ySize (2)` `-xZF (2)` `-yZF (2)`
vRev	0	Reverse the order of points in an nmrWish floating-point binary data array.
vSin	0	Apply function to nmrWish floating-point binary data: sine.
vSort	3	Sort the values in an nmrWish floating-point binary data array.
vStdDev	3	Find the standard deviation of values in an nmrWish floating-point binary data array.
vSum	27	Find the average of values in an nmrWish floating-point binary data array.
vSurface	72	Add a term to a ramachandran distribution; used to general phi/psi surfaces for chemical shifts, etc.	`-sPtr (72)` `-val (72)` `-xSize (72)` `-ySize (72)` `-xfw (72)` `-yfw (72)` `-x0 (72)` `-y0 (72)` `-dPtr (27)`
vsAdd	0	Scalar operation on nmrWish floating-point binary data: add a constant.
vsDiv	7	Scalar operation on nmrWish floating-point binary data: divide by a constant.
vsFix	2	Scalar operation on nmrWish floating-point binary data: set data to zero if its absolute value is less then or equal to a constant.
vsIntegLoc	5	Find the location of the point where the integral (simple sum) of an nmrWish floating-point binary data array becomes larger then a given constant.
vsMult	15	Scalar operation on nmrWish floating-point binary data: multiple by a constant.
vsPower	0	Scalar operation on nmrWish floating-point binary data: raise to a power.
vsSet	21	Scalar operation on nmrWish floating-point binary data: set values to a constant.
vsSub	0	Scalar operation on nmrWish floating-point binary data: subtract a constant.
vvAdd	3	Vector-Vector operation on floating-point nmrWish binary data: addition.
vvCast	2	Vector-Vector operation on floating-point nmrWish binary data: type conversion (such as integer to float).
vvDiv	2	Vector-Vector operation on floating-point nmrWish binary data: divide.
vvDot	14	Vector-Vector operation on floating-point nmrWish binary data: dot product.
vvMove	18	Vector-Vector operation on floating-point nmrWish binary data: copy.
vvMove2	4	Multiple vector copying for floating-point nmrWish binary data.
vvMult	32	Vector-Vector operation on floating-point nmrWish binary data: multiply.
vvSub	5	Vector-Vector operation on floating-point nmrWish binary data: subtract.
vvSwap	0	Vector-Vector operation on floating-point nmrWish binary data: exchange contents of two vectors.
writeImage	22	Create and save an image in TIFF format using three nmrWish spectral data arrays for the red, green, and blue channels. See also: readROI, Stand-alone program pcaNMR, nmrWish function pcaNMR.	`-out (22)` `-x (13)` `-y (13)` `-gif (11)` `-roiR (9)` `-roiG (9)` `-roiB (9)` `-tiff (4)` `-iRMax (3)`
writeROI	169	Write a spectral data region-of-interest (ROI) as NMRPipe-format data.	`-roi (168)` `-out (168)` `-ov (158)` `-verb (14)` `-help (1)`

NMRWish TCL Library Procedures

Name	Instances	Description	Common Arguments (Instances)
arg2array	0	Store a list of arguments on the command line in a TCL array.
dynEvalTensor	0	Compute Dipolar Coupling or Pseudo-Contact Shift tensor parameters for a timestep in a DYNAMO molecular structure calculation.
dynExit	36	Exit from a DYNAMO molecular structure calculation.
dynGetPDBDisuList	2	Identify atom pairs likely to be involved in S-S bonds from a PDB file read as a DYNAMO object.
dynGetPDBSeqStr	7	Create DATA SEQUENCE lines from the residue sequence in a PDB file read as a DYNAMO object.
dynNAAngles	0	Extract angles associated with Nucleic Acid PDB file read as a DYNAMO object.
dynReadGMC	61	Read a DYNAMO molecular structure calculation GMC environment (GMC, Generic Molecular Coordinates).	`-gmc (61)` `-pdb (61)` `-r1 (28)` `-rN (28)` `-torsion (27)` `-ac (9)` `-uangle (1)` `-noe (1)`
dynSimulateAnnealing	60	Perform a DYNAMO Simulated Annealing Calculation with Initialization, High-Temperature, and Cooling Stages.	`-graph (59)` `-print (59)` `-sa (59)` `-fc (56)` `-rasmol (47)` `-nocenter (19)` `-notensorProc (16)` `-tensorProc (12)` `-norasmol (8)`
estSpecNoise	12	Estimate the standard deviation of the baseline noise in the named NMRPipe-format data.
expand	0	Expand a string into a list of its individual characters.
extractArray	0	Extract all index/value pairs from an array.
extractSaupe	8	Dipolar Coupling Analysis Utility
findClusters	5	Cluster Analysis on Objects in a List
flagLoc	1298	Find the location of a flag in the command line.
get15NDim	11	Return the axis name of the 15N dimension in an NMRPipe-format header.
get15NTabVar	21	Get the name of the variable (column) in an NMRPipe-format peak table associated with amide-nitrogen (15N) chemical shift in PPM.
getAbsMax	6	Return the value with the greatest absolute value in a list.
getAbsMin	0	Return the value with the smallest absolute value in a list.
getArgD	2525	Extract the named argument's value from the command line if it can be found.
getArgDN	32	Set a TCL array variables from an argument's value in the command line if it can be found.
getArrayList	2	Extract array contents as a list.
getAtomEntry	4	Find an atom's entry (row number) in a PDB file.
getAvg	72	Return the average of values in a list.
getAvgAngle	31	Returns the average of a list of angles in degrees.
getChi2	0	Computes the chi-square statistic on the difference between two lists, given the corresponding uncertainties.
getChiAngle	2	Extract chi sidechain angles for a given residue in a PDB file.
getDefinedAngles	3	Returns a list of angles in degrees with "undefined" values (> 999) removed.
getDim	0	Return the dimension location (1, 2, etc) associated with the axis name in an NMRPipe-format header.
getDimKeyword	18	Return the keyword (CUR_XDIM, CUR_YDIM, etc) associated with the axis name in an NMRPipe-format header.
getDirectDim	11	Return the axis name of the directly-acquired dimension in an NMRPipe-format header.
getEListAvg	13	Get the average of values for a GDB database table variable (column) from a list of entries (rows).
getEListMax	0	Get the maximum value of a GDB database table variable (column) from a list of entries (rows).
getEListMin	0	Get the minimum value of a GDB database table variable (column) from a list of entries (rows).
getEListStat	11	Apply a given TCL function to compute a statistic using a list of entries (rows) from a GDB database table.
getEListStdDev	0	Get the standard deviation for a GDB database table variable (column) from a list of entries (rows).
getEListSum	0	Get the sum of values for a GDB database table variable (column) from a list of entries (rows).
getEListVals	0	Extract all values associated with a GDB database table variable (column) from a list of entries (rows).
getFileBytes	6	Returns the size of a file in bytes, with options for compressed data.	`-estimate (3)` `-exact (1)`
getFirstLevel	6	Calculate a contour height from a range.
getFormat	0	Reformat values in list, for example to give a uniform number of decimal places.
getHNTabVar	21	Get the name of the variable (column) in an NMRPipe-format peak table associated with amide-proton (HN) chemical shift in PPM.
getHist	4	Build histogram values for lists of X/Y pairs.
getIndirectDim	8	Return the "third dimension" axis name in an NMRPipe-format header for amide-detected 3D data.
getIndirectTabVar	14	Get the name of the variable (column) in an NMRPipe-format peak table associated with the "third" dimension chemical shift of an amide-detected 3D data.
getIota	0	Return a numeric list with equal spacing between values.
getKeyData	26	Get the DATA information associated with a given keyword.
getListArgD	307	Extract the named argument's list of values from the command line if it can be found.
getMax	97	Return the maximum value in a list.
getMaxRes	15	Extract the largest residue number from a PDB file read as a GDB database table.
getMedian	27	Return the median of values in a list, return value is an average of two values for lists with even numbers of points.
getMin	79	Return the minimum value in a list.
getMinRes	14	Extract the smallest residue number from a PDB file read as a GDB database table.
getNAAngles	2	Extract angles associated with Nucleic Acid PDB file read as a GDB database table.
getNAResName3	0	Return the 3-character residue name associated with the given nucleaic residue name.
getNthResName	29	Get the name of the given residue in a PDB file.
getNthTensor	79	Extract tensor parameters from a Dipolar Coupling result.
getOmegaAngle	9	Extract omega backbone angles for a given residue in a PDB file.
getPChi	2	Return the Chi-square probability given a list of residuals, their associated uncertainties, and the number of degrees of freedom.
getPDBDisuList	2	Identify atom pairs likely to be involved in S-S bonds from a PDB file read as a GDB database table.
getPDBSeqList	3	Extract sequence information from a PDB file read as a GDB database table.
getPDBSeqStr	0	Create DATA SEQUENCE lines from the residue sequence in a PDB file read as a GDB database table.
getPDF	5	Create a 1D probability density distribution from lists of X/Y pairs.
getPDFCoords	4	Get coordinates for the X-axis of a 1D probability density function.
getParmI	93	Extract an integer parameter from an NNRPipe-format header.
getPearsonR	12	Return the Pearson's R correlation coefficient.
getPhiPsiAngles	18	Extract phi/psi backbone angles for a given residue in a PDB file.
getQuadSize	4	Return 1 if the given dimension is real-only, 2 if complex.
getRMS	48	Return the RMS (Root Mean Square) of values in a list.
getROIStat	14	Perform a computation on intensities from a given spectral region-of-interest (ROI.
getRange	0	Return the range (maximum - minimum) of values in a list.
getRepeat	0	Create a list by repeating a value.
getResName1	36	Return the 1-character residue name associated with the given amino acid residue name.
getResName3	19	Return the 3-character residue name associated with the given amino acid residue name.
getReverse	2	Returns a list with the order of its items reversed.
getSaupeAngle	17	Compute the angle between two Dipolar Coupling alignment tensors.
getScale	0	Return the value that minimizes the residual between values in two lists.
getSeqList	62	Extract residue sequence information from DATA statements in a table into a TCL array.
getSeqListSeqStr	2	Create DATA SEQUENCE lines from the residue sequence list.
getSequence	0	Extract the protein residue sequence from a PDB file read as a GDB database table.
getSimpleMedian	0	Return the median of values in a list; return value is always an element from the list.
getSpecRange	0	Find the ranges of intensities in an NMRPipe-format data file.
getStdDev	56	Return the standard deviation of values in a list.
getStdDevAngle	36	Returns the standard deviation of a list of angles in degrees.
getSum	18	Return the sum of values in a list.
getSumSq	8	Return the sum of squares of values in a list.
getTabAvg	3	Get the average of values of a variable (row) in a GDB database table.
getTabKeyItem	0	Get the value associated with a given DATA keyword in a table.
getTabKeyLength	3	Get a number of items associated with a DATA keyword in a table.
getTabKeyList	0	Get a list of DATA keywords in a table.
getTabMax	32	Get the maximum value of a variable (row) in a GDB database table.
getTabMin	26	Get the minimum value of a variable (row) in a GDB database table.
getTabStat	0	Apply a given TCL function to compute a statistic using all values extracted from a GDB database table variable (column).
getTabStatU	2	Apply a given TCL function to compute a statistic using all values extracted from a GDB database table variable (column), with undefined values skipped.
getTabStdDev	0	Get the standard deviation of values of a variable (row) in a GDB database table.
getTabSum	0	Get the sum of values of a variable (row) in a GDB database table.
getTabTextCount	0	Get the number of text items in a table.
getTabTextInfo	0	Extract table text items into a TCL array.
getTabVals	7	Extract all values associated with a GDB database table variable (column).
getTau	2	Extract the Tau value from the given NMRPipe-format data file.
getVsStat	12	Computes a statistic on the difference of two numerical lists of the same length.
getWAvg	24	Return the weighted average of values in a list.
getWRMS	6	Return the weighted RMS (Root Mean Square) of values in a list.
initMiniPlot	11	Initialize settings for multiple "postage stamp" PostScript plots.	`-landscape (1)` `-pxn (1)` `-bwx (1)` `-bwy (1)` `-bdx (1)` `-bdy (1)` `-bg (1)`
initResNames	48	Initialize the list of canonical residue names for common amino acids.
isAscending	0	Return 1 if the given numerical list is ascending.
isDescending	0	Return 1 if the given numerical list is descending.
isFlag	5	Return 1 if argument is a valid flag.
isInt	4	Test if argument contains only one or more digits 0-9.
isMonotonic	0	Return 1 if the given numerical list is monotonic.
linterp	0	Interpolate XY pairs in numerical lists.
listDisjoint	4	Returns the unique elements in one list but not in the other.
listIntersect	6	Returns the unique elements common to two lists.
listUnion	6	Returns the unique elements in the combined contents of two lists.
listUniq	6	Returns the unique members in a list.
loadArray	3	Read the contents of a TCL array from a file.
loadArrayDB	0	Read the contents of one or more TCL arrays from files in a directory.
lselect	22	Select items in one list according to 1 and 0 values in a corresponding list.
metro	0	Combinatorial optimization by metropolis method.
name2fmt	0	Convert a file name to an NMRPipe format template (i.e. test001.dat to test%03d.dat).
nextFlag	9	Find the location of the next flag in the command line.
nextMiniPlot	11	Prepare to draw the next "postage stamp" plot.
nextPower2	3	Return the smallest power of two equal to or greater than the given argument.
okExit	8	Display a Dialog Box asking permission to exit an application.
okWrite	7	Display a Dialog Box asking permission to overwrite a file.
pdbNAAngles	0	Extract angles associated with Nucleic Acid structures.
permList	8	Form all permutations of the elements in the given list taken N at a time.
polySolve	0	Return the solution coefficients to a polynomial least squares problem.
probePDBSrc	0	Identify PDB file contents as protein or nucleic acid.
rClip	17	Clip a variable's value.
rOrder	3	Numerical Utility
rSwap	0	Swap the contents of two TCL variables.
rdFDATA	65	Read the NMRPipe-format header from the named file.
rdFDATAU	6	Read the NMRPipe-format header from a data file opened for reading.
removeElement	0	Remove an element from a list by its location.
removeNullElements	2	Remove null items from a list.
sameList	2	Test whether two lists have the same unique members.
setArgD	30	Change the value of an argument in the command line if it can be found.	`-xLAB (6)` `-yT (6)` `-yMODE (6)` `-yLAB (6)` `-aq2D (6)`
setColors	3	Set some typical colors used for graphical interface items such as buttons. OBSOLETE.
setFlag	0	Change a flag in the command line.
setFlagD	0	Change a flag in the command line if it can be found.
setFonts	41	Set some typical font names for use in an NMRWish graphical application.
setListArgD	6	Change an argument's list of values in the command line if it can be found.	`-comment (6)`
setOSType	38	Set some operating-system dependent variables. OBSOLETE.
showError	79	Display a Dialog Box indicating an error.
simplePermutation	4	Form all permutations of the elements in the given list.
simplePermutationN	0	Form all permutations of the elements in the given list taken N at a time.
storeArray	4	Save the contents of a TCL array as a file.
storeArrayDB	0	Save the contents of one or more TCL arrays as files in a directory.
wrFDATA	3	Write the NMRPipe-format header to the named file.

Frank Delaglio, Ph.D.