Scripts of the NMRPipe System

This particular reference page lists the application scripts of the NMRPipe system. These are generally either UNIX C-shell scripts (with the .com extension), or NMRWish TCL scripts (with the .tcl extension). For example, the script autoFit.tcl is used to perform general-purpose multidimensional lineshape fitting.

In many cases, scripts are invoked directly at the UNIX command line. Some scripts are used frequently. Some, however, may rarely be used, were added only for development purposes, or may be superseded by other facilities. In an attempt to indicate which scripts 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 script in recorded examples of both routine use and research and development of the software. Note that this underestimates the use of scripts which are more often used interactively.

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.

Frank Delaglio, Ph.D.