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p: pp - interactive sets - up every thing for peak picking and realizes it permits peakpicking in a interactive, graphical manner.
PAGE: PAGE plot_file_name This command appends code at the end of plot_file_name for page ejection; closes the plot file; and send it to the plotter.
PCOLOR: PCOLOR color_index plot_file_name This command permit to change the color mode when plotting on a color Postscript printer. On HPGL PCLOR and PEN are equivalent. color_index is : 1:black 2:red 3:yellow 4:green 5:cian 6:blue 7:purple 8:white
PEAK: PEAK output {radius} Will generate a peak-table from the current data set, output can be either a file-name or *screen. Peaks are located if their intensity lies within the margin defined by the MINIMAX command. In 2D, PEAK will prompt you for a "packing radius". Peaks which lies within a distance equal or smaller than this packing radius (in points) will be ignored in favor of the larger peak in this radius. The command SHOWPEAK will show you on the display where the peaks have been found. The command PKLIST will list the peak table contents. This is the peak-picker form the PARIS integrator.
peak_pick: peak_pick - interactive (replaces pp) sets - up every thing for peak picking and realizes it permits peakpicking in a interactive, graphical manner.
PEN: Pen n plot_file_name Selects the pen number n on the plotter. On a postscript laser printer, this corresponds to different line width and dash patterns.
PH: PH is an interactive 1D phasing module. A button window pops-up which permits the user to adjust the 0th and 1st order phase. The 1st order pivot point is set by clicking in the 1D Spectrum window. If you exit by clicking in Ok the phase correction is applied, and the phase values becomes then the default values for the PHASE command. If you exit with Cancel, no phase correction is applied and the original data is restored.
ph2dc: interactive permits to phase a 2D in F1 by interactively selecting columns and building a composite 1D
ph2dr: interactive permits to phase a 2D in F2 by interactively selecting rows and building a composite 1D
PHASE: PHASE X Y {dim) Permits to modify the phase of the current displayed spectrum. You have to enter zero-order (X) and first-order (Y) corrections, and dimension (dim) in 2D. Values are in degree, and first-order correction uses center point as pivot. For 1D data an interactive phase command is available : PH.
PK->DT: Computes a pseudo-FID from the peaks parameters s held in the PEAK() table. Permits to display a spectrum computed by LP analysis.
pkadjust: pkadjust line_shape with line_shape lorentzian / gaussian adjust each peak in the table by fitting around it
PKCLEAN: pkclean min_int Will remove from the pak table entries with intensity less than min_int
PKCLEAR: This command remove all entry from the current peak table.
PKLIST: pklist i j List the contents of the current peak table, from entry i to entry j.
PKPROJ: PKPROJ axis alogrithm tolerance Propagates the contents of the 2D peak-table on the 1D peak-table. All the 2D peaks will generate an entry in the 1D table. If two (or n) peaks are less than tolerance (in Hz) apart during the projection, they will be merged into one peak. The intensity of the resulting peak will be either the mean value ot the max value of the initial peak, depending on the chosen algorithm (Mean or Skyline). PKPROJ does not modify the spectral parameters (spectral width, frequences and offsets), so, if the 1D spectral parameters are different from the 2D parameters, strange results can be obtained.
PKREAD: PKREAD file_name yes/no Reads a peak list file created with PKWRITE into internal peak list. Depending on the option, the read values are appended to the current value (no) or the peak table is cleared before reading the file.
PKRESET: This command recompute peak intensities from the current data set and the current peak table, giving results equivalent to PEAK. Usefull when either the data-set or the peak table has changed. Note that PKREAD reads in the whole peak table, including intensities, thus PKRESET permits to recompute intensities form a stored table.
PKRM: PKRM index Remove the peak index in the current peak table.
pkrmi: pkrmi interactive this macro permits to interactively and graphically remove peaks from the peak table
PKSELECT: PKSELECT index() Select the peaks parameters whose index() are given. To end selection, enter the index 0.
PKSYM: PKSYM param tolerance Symmetrize in the 2D peak-table by either removing (param=0) entries in the peak table that do not have a symmetrical counterpart, or by adding (param=1) a symmetrical peak in the table. The presence or absence of a symmetrical peak is checked within a window of tolerance (in Hz) around the peak. PKSYM does not modify the spectral parameters (spectral width, frequences and offsets), so, if they significally different on the both axis, strange results can be obtained.
PKWRITE: PKWRITE file_name Writes the contents of the peak table on a file. The table can then be read with the PKREAD command.
PLANE: PLANE axis index In 3D only. Permits to select a plane from the 3D buffer and copies it to the 2D buffer. Axis is either F1, F2 or F3 as the axis orthogonal to the chosen plane. Thus F1 selects plane F23, etc...
planeint: interactive permits to choose a plane interactively on a 3D by clicking on the 1D typically, the 1D should come from a vert command (or equivalent direction) and the currently displayed plane determines the direction
PLOT: plot plot_file_name Plots the current spectrum on the plotter, using the current value of contexts (see PLOT?). If in 1D, plot the 1D spectrum If in 2D, plot the contour-plot, as displayed with the CDISP2D command. If in 3D, plot the currently selected plane, as displayed with the CDISP2D command. will create a plot file named file_name, which can later be plotted by the command Gifa> PAGE plot_file_name If your GIFA program is working in postscript (check with the CONFIG command), and if you have a postscript previewer (IBM, Silicon Graphics, some X-stations) then you can display the contents of your plot-file before sending it to the plotter. The filename *s will send the plot to the screen rather than to a file or the plotter. The file name *PL will create a temporary plot file that will be deleted after plotting.
PLOT3D: plot3d plot_file_name Equivalent to the PLOT command, will generate a 3D plot, equivalent to the display obtained with the DISP3D command.
plot?: PLOT? interactive prompt for parameters for plotting
PLOTAXIS: PLOTAXIS direc output This command plots a set of axis on its output. The axis are 0.5 cm below the current plotoffset. If direc=F1 a vertical axis is drawn If direc=F2 a horizontal axis is drawn If direc=F12 both axes are drawn PLOTAXIS uses the current SPECW and OFFSET for the axis calibration.
PLOTAXIS?: This command prompts you for different parameters that will be used by PLOTAXIS : unit (may be different of the UNIT command) and separations on x and y axes. The definition is also used for the GRID command.
plotcolordisp: plotcolordisp <Filename> Makes a color contour plot on plotter
PLOTLINE: PLOTLINE X1 Y1 X2 Y2 plot_file Draws a line from the X1 Y1 point to the X2 Y2 point (in cm, relative to PLOTOFFSET).
PLOTLINES: PLOTLINES X1 Y1 X2 Y2 plot_file Draws a line from the X1 Y1 point to the X2 Y2 point (in index unit, projected on the CX x CY area, as used by the PLOT command).
plotn: plotn total_cx total_cy partial_cx partial_cy y/n plot on several pages to fit size permits to build large composite plots on size limited plotters
PLOTOFFSET: PLOTOFFSET x y Values are used to offset the (0,0) origin of the plot at (x,y). Permits to draw several plots on the same page, or to leave room for axes. Default values are 1 1 (in cm).
PLOTPEAKS: will plot on the plot file, the contents of the internal peak table, thus permitting to plot the result of the PEAK command.
PLOTTER: PLOTTER H(P-GL) / p(ostscript) Permits to select which kind of output will be generated ans using all the plot commands. HP-GL or postscript code can be selected. If the gifaplot shell script has been correctly st-up, the correct output should be sent to the correct plotter with no user intervention.
PLOTTEXT: PLOTTEXT string X Y plot_file Sends the string "string" to the plot_file, at the X, Y position (in cm, relative to PLOTOFFSET)
PLOTTEXTS: PLOTTEXTS string X Y plot_file Sends the string "string" to the plot_file, at the X, Y position (in index unit, projected on the CX x CY area, as used by the PLOT command)
plot_fit: to make a nice multicolored plot out of the fitted line shapes
PLUS: Sets to zero the negative part of the data set.
point: interactive mode on screen Permit to interactively inspect the content of the data-set, using the mouse on the graphic-screen. Exit when you click the 3rd button of the mouse Clicked point are stacked onto the POINT_STACK
POINT->PK: This command will add the point in the point stack (set by the user with the last point or MONOPOINT command), into the current peak table.
POINT_CLEAR: clears the point stack
point_cross: interactive mode on screen Permit to interactively inspect the content of the data-set, using the mouse on the graphic-screen. Exit when you click the 3rd button of the mouse Clicked point are stacked onto the POINT_STACK that one draws a little cross
point_dump: dumps the containt of the point stack
POINT_INPUT: POINT_INPUT F1 {F2} A point with coordinates F1 (in 1D, or F1,F2 (in 2D) is put on the top of the point stack.
POINT_POP: remove one entry from the point stack.
POINT_PUSH: Add one entry into the point stack. The point stack contains spectral coordinates, which can be used within macros, and are also used by certain commands (typically BCORR). Whithin macros, the content of the point stack can be examined with the context variables : $npoint; $pointx[i]; $pointy[i] The POINT_CLEAR command empties the stack. The MONOPOINT command sets the top entry on the stack. The POINT_PUSH command push the entry on the top, thus duplicating the entry, and adding an entry in the stack. The POINT_INPUT command permits to enter a value with determined values The POINT_POP command pops one entry in the stack. The macro point permits fill the stack by clicking on the spectra The macro point_dump permits to dump the content of the stack
pp: pp - interactive sets - up every thing for peak picking and realizes it permits peakpicking in a interactive, graphical manner.
PRIMER: The GIFA program is a multi-purpose NMR program. It is designed for the processing and the display of 1D and muti-dimensional NMR data-sets. The program includes sophisticated signal processing methods such as Maximum Entropy processing, Linear prediction, line fitting, complete control language, or 2D peak integrator as well as more classical processing, displaying and plotting of NMR experiments. It can handle the complete study of a set of NMR multidimensionnal data-sets, from the raw data to plotting, visualisation, and finally give some help to the assignment process. In contrast with most NMR programs, Gifa tends to do as much data processing as possible in memory. Thus a typical processing session consists in : * transfering the raw data-set from the spectrometer to the processing computer and converting it to a gifa-compatible format, for instance with the ux2gifa shell script. * loading the data-set in memory with the command READ * apodizing the data set with EM (exponential), GM (Gaussian), TM (trapezoid), SIN (shifted sine bell) or SQSIN (squared shifted sine- bell). * changing the size of the data set (zero filling or truncature) with CHSIZE. * realizing the Fourier transform in the acquisition dimension with ft_sim (simultaneous acquisition) or ft_seq (sequential acquisition); and in the non-classical dimension with ft_tppi (TPPI acq.), ft_sh (States-Haberkorn acq.), ft_sh_tppi (mixed mode) or ft_phase_modu (phase modulation) (there are als the basic commands : FT, RFT, FTBIS, IFT, IRFT, IFTBIS, REVF, INVF). * correcting the phase with PH (interactive), ph_2dc and ph2dr (interactive in 2D), PHASE or HPHASE (batch); or taking the modulus with MODULUS. * eventually correcting the base line with BCORR (see help for that command) * contour plot as well as density plot are available for 2D's. There is even an on-screen stacked plot available. * rows and columns from 2D's can be examined : rowint, colint (interactive); ROW, COL, DIAG; as well as planes and lines from 3D's planeint, vertint, PLANE, VERT, DIAG. You should also know that : o 1D, 2D and 3D processing can be selected o plots are available on postscript as well as HP-GL o there is a peak-picker in 1D, 2D and 3D, as well as a line-fitter (in 1D so far) o MaxEnt and Linear Prediction are available with a comprehensive set of commands o you can write your own commands with the command langage o you can even set-up your own graphic interface with the BUTTONBOX command. Try also : * HELP a_given_command / for instance : help ft * apropos a_given_topic / for instance : apropos transform * reading the manual
PRINT: PRINT string This command permits to issue a string to the user. Permits interactivity in command file.
printf: printf format_string arg1 arg2 ... * realises the equivalent of a C `printf' all the remaining of the line up to the star is taken as arguments
proc2d: proc2d sourcefile destinationfile axis_to_process commands this macro processes a 2D file using the cache system (join, getc, putc) it permits to handle very large files, which would not fit into memory. sourcefile : is the initial data-set destinationfile : is the result of the process axis_to_process : either F1 or F2 (NOT F12) commands : the commands to be applied to each row/column in 1D notation the commands are the regular commands you would used to process a 1D data-set. when called without parameters, 'commands' can be several line long, as typed when proc2d is called with parameters on the line, then 'commands' should be a single command line within quotes. e.g. proc2 my_ser_file my_F2_processed F2 'sin 0.2 ft_sim phase 30 -40 real bcorr 3' proc2 my_F2_processed my_F12_processed F1 'sin 0.2 revf ft phase 0 30 real bcorr 3' would process a whole 2D in 2 steps.
proc3d: proc3d sourcefile destinationfile plane_to_process commands this macro processes a 3D file using the cache system (join, getc, putc) it permits to handle very large files, which would not fit into memory. sourcefile : is the initial data-set destinationfile : is the result of the process plane_to_process : either F1, F2 or F3 (NOT F12 or F123) commands : the commands to be applied to each plane in 2D notation the commands are the regular commands you would used to process a 2D data-set. when called without parameters, 'commands' can be several line long, as typed when proc3d is called with parameters on the line, then 'commands' should be a single command line within quotes. e.g. proc3 ser_file F1_proc F1 'sin 0.2 f12 ft_sim phase 30 -40 f2 real f12 ft_tppi ' process axes f3 and f2 as 2D proc3 F1_proc full_proc F2 'sin 0.2 f1 ft_tppi real f1 bcorr 3 f1' process axis f1 would process a whole 3D in 2 steps.
proc3d_form: prepares a form for proc3d
PROJ: PROJ n a Permits to perform a projection of 2D data-set. Projections are done either along F1 (n=1) or F2 (n=2) axes, with either skyline (a=s) or mean (a=m) technic.
proj3d: proj3d file axis algo axis is F1, F2 or F3 algo is M or S equivalent to proj in 3D, but on joined file
PUT: PUT parameter {n} Moves the content of the current buffer to an other buffer With parameter equal to: -DATA: load the data to be used for MaxEnt processing in 1D -FILTER: load the filter used for Deconvolution. If NCHANNEL is greater than 1, then which channel you want to put. eg. PUT FILTER 3. PUT FILTER 0 will consider the current data set as the multichannel filter, and will load the whole filter. Useful when associated with GET FILTER to store filters as files. -WINDOW: load the window to be used for MaxEnt processing in 2D only -ROW n : load the 1D buffer in the ROW n -COL n : load the 1D buffer in the COL n -AMOEBA : the mask definition to be used by the next MSKINTEG command in 3D only -PLANE Fx n : load the 2D buffer in the plane Fx n
PUTC: syntaxe depends on the dimentionnality of the currently joined data- set (to) and on the current context dim (from) : 1D to 1D : PUTC left right 1D to 2D : PUTC axis index left right 1D to 3D : PUTC axis index1 index2 left right 2D to 2D : PUTC left1 left2 right1 right2 2D to 3D : PUTC axis index left1 left2 right1 right2 3D to 3D : PUTC left1 left2 left3 right1 right2 right3 Writes into the currently connected file, the area of data as described.
PUTHEADER: PUTHEADER param_name value Set the value of a parameter associated to the currently JOINed data-set. If the parameter already exists, the value is changed, otherwise it is created. Any parameters can be used. Gifa already uses the following parameters (as listed with the dataset command) : Frequency, Freq1, Freq2, Freq3, Specw1, Specw2, Specw3, Offset1, Offset2, Offset3, Type, Dim. But you can use any other parameter name if you wish.
pwd: as in unix

Back to Alphabetical List

p

PAGE

PCOLOR

PEAK

peak_pick

PEN

PH

ph2dc

ph2dr

PHASE

PK->DT

pkadjust

PKCLEAN

PKCLEAR

PKLIST

PKPROJ

PKREAD

PKRESET

PKRM

pkrmi

PKSELECT

PKSYM

PKWRITE

PLANE

planeint

PLOT

PLOT3D

plot?

PLOTAXIS

PLOTAXIS?

plotcolordisp

PLOTLINE

PLOTLINES

plotn

PLOTOFFSET

PLOTPEAKS

PLOTTER

PLOTTEXT

PLOTTEXTS

plot_fit

PLUS

point

POINT->PK

POINT_CLEAR

point_cross

point_dump

POINT_INPUT

POINT_POP

POINT_PUSH

pp

PRIMER

PRINT

printf

proc2d

proc3d

proc3d_form

PROJ

proj3d

PUT

PUTC

PUTHEADER

pwd