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SCALE: SCALE x Changes display scale factor. Default value is 1. The data-set is multiplied by SCALE before display. The larger the SCALE, the higher the spectrum will be. Used by all graphical output, either on screen or on plots.
SCALE3D: SCALE3D x This context is used to reduce / expand the drawing during a 3D display, usually a value smaller than 1 is needed to fit the whole cube within the graphic window.
SCOLOR: scolor index Determines the color used by the SHOW command index is : 1:white 2:red 3:yellow 4:green 5:cian 6:blue 7:purple 8:black
SEGM1: SEGM1 n choose the way the first segmentation is done in BCORR 3 . 0 : without. 1 : with a standard deviation algorithm on the data set. 2 : with a standard deviation algorithm on the first derivative of the data set. 3 : with thresholds on the data set, and on the first and second derivatives. 4 : with a dynamic clusters algorithm. +10 : with a morphological filtering after the segmentation.
SEGM2: choose the way the second segmentation is done in BCORR 3. This feature is only useful with a polynomial approximation. 0 : without. 1 : interactive. 2 : automatic. When you choose an interactive second segmentation, you have to choose one or several areas with the WINDOW command to allow the program to cut the correction in these areas if needed. The automatic segmentation uses a window, WINSEGM2, and a threshold, LEVELSEGM2.
SET: SET variable_name = value SET static_variable := value Assigns the value of the variable variable_name to value. Creates the variable if it does not already exist. Note that you should not use a $ sign before variable_name. value can be any kind of value : number, string, read from a file, another variable, a calling parameter ($_) or an evaluated expression. If value is missing, or if $_ is used and no parameter are available, the user is prompted for input. When the variable is created during the execution of a macro, the first syntax creates a local/volatile variable which value cannot be accessed by subsequent called macros, and that will be removed at the end of the macro. The second syntax creates a global/static variable that can be accessed by any macros, and that will remain until explicitly removed with the UNSET command.
SETPATH: SETPATH new_path_string Permits to change the current GifaPath used for calling macros. The new_path_string contents all the directories in which macros file will searched for, the list is blank separated. The content of the current GifaPath is held into the $GIFAPATH context. So the following is a very typical use for adding an address SETPATH ("new_directory"; $GIFAPATH)
SETPEAK: SETPEAK index F1 { F2 { F3 } } Permit to modify directly the content of the peak table. The number of entries depends whether you are in 1D, 2D or 3D. The peak entry at index is modified in the current peak table. Only coordinates are given, intensity is taken form the data-set, widthes and other parameters are lost. This is not the way for adding new peaks in the peak table, use POINT_INPUT POINT->PK instead.
SETPROMPT: SETPROMPT new_prompt_string Permits to modify the prompt used in the text window.
SETVAL: setval i { j { k } } x Will set the value of the data point to x. The number of coordinates of the point depends of dim. In dim 2 or 3, coordinates are F1 F2 or F1 F2 F3. Can be usefully used when associated to the functions valnd() to change data point value.
SH: SH string Will pass the string to the operating system. For instance, used by macros such as pwd, ls, more, etc... SH alone will enter the Operating system
SHIFT: This context holds the systematic baseline shift of the current data-set, computed automatically by EVALN. Used by INTEG.
SHOW: SHOW parameter Displays graphically extra information without disturbing the content of the working buffer. Uses the current definition of SCOLOR for drawing. With parameter equal to: -WINDOW: display actual window used to compute the chisquare -FILTER: display filter used for Deconvolution -LAMB: display evolution of Lambda during MaxEnt iteration -ENT: display evolution of Lambda during MaxEnt iteration -CHI: display evolution of Lambda during MaxEnt iteration -STEP: display evolution of Lambda during MaxEnt iteration -SUM: display evolution of Lambda during MaxEnt iteration -CONV: display evolution of Lambda during MaxEnt iteration -FT: display evolution of Lambda during MaxEnt iteration -RESIDUE: displqy the residue of the spectrum after a MaxEnt run -CURRENT: moves the current displayed image to the other window -LINEFIT: the result of the last line-fitting computation -AMOEBA: the mask used by the last INTEG command
SHOWC: SHOWC scale display the currently JOINed file using the current zoom window (redefined in ppm and used on the JOINed data-set) The current parameters are used for the display (VHEIGH, LEVEL, etc..) but not SCALE which is passed to the command. In 2D the display is only showed in the controur window. The command is not implemented in 3D yet. This command is used by the super1d / super2d macros to display several spectra on screen.
SHOWLINE: showline x1 y1 x2 y2 Will draw a line on the displayed spectrum. Coordinates are in index values. The line will be drawn accordingly to the zoom mode. When in 2D with density plot and contour plot both on, the contour plot will be used for display. Uses the current definition of SCOLOR for drawing.
SHOWPEAK: showpeak index will display on the current graphic, the indexth peak of the peak table. Uses the current definition of SCOLOR for drawing.
SHOWPEAKS: will display on the current graphic, the contents of the internal peak table, thus permitting to visualize the result of the PEAK command.Uses the current definition of SCOLOR for drawing.
SHOWTEXT: SHOWTEXT string X Y Displays the string "string" on the displayed spectrum, at the X, Y position. Coordinates are in index values. When in 2D with density plot and contour plot both on, the contour plot will be used for display. Uses the current definition of SCOLOR for drawing.
show_fit: to make a nice multicolored plot out of the fitted line shapes
SIGN: SIGN -1 / 0 / 1 Tells the program how to display 2D data-sets. Used by DISP2D, CDSIP2D and PLOT commands if 1, 2D program will display only positive levels, if -1, 2D program will display only negative levels, if 0, 2D program will display both positive and negative levels,
SIGN_PEAK: SIGN_PEAK 1 / -1 Indicates to PEAK and to INTEG to search for positive or negative peaks.
SimSpect2D: Macro to simulate a 2D spectrum from an intensity file and a DBM ppm file, used by SimSpect2D_form SimSpect2D dbm_ppm_filename intensity_filename F1_modulation Symetrical_option the ppm DBM file can be generated from an ascii ppm file by the macro mkdbppm the ascii intensity file has the following free-format: INT residu_name1 residu_number1 atom_name1 residu_name2 residu_number2 atom_name2 intensity_value F1_modulation can be either sh_tppi or phase_modu if Symetrical_option is sym, then each entry in the intensity file is duplicated on the other side of the spectral diagonal.
SimSpect2D_form: SimSpect2D_form args... builds and apply a standard action for 2D spectrum simulation
SIMU: Simulate data, works in 1D in 2D and in 3D You will be prompted for input. SIMU memorizes the last used values so SIMU %% is a valid syntax.
SIMUN: (1D) simun ampl linecoord linewidth phase (2D) simun flg ampl linecoordf1 linecoordf2 linewidthf1 \ linewidthf2 phasef1 phasef2 (3D) simun ampl linecoordf1 linecoordf2 linecoordf3 \ linewidthf1 linewidthf2 linewidthf3 phasef1 phasef2 phasef3 Simulate data, works in 1D in 2D and in 3D You will be prompted for input. One line is simulated at each run, and is added to the data. The line coordinates are entered in PPM, Hz or Index, according to the unit value. The line widthes are in Hz. The 1D and 3D data are complex in all dimensions, the 2D data can be phase or amplitude modulated, depending on flg : flg = 0 : the data are simulated in phase modulation flg = 1 : the data are simulated in amplitude modulation SIMUN memorizes the last used values so SIMUN %% is a valid syntax.
SIMUNOE: This command is now obsolete, it has been superseded by the SimSpect2D macro which realizes the same action. This command permits to simulate a 2D data set from the result of a program computing NOESY intensities (such as CORMA). It will prompt you for the filename of the Corma output file, the filename of the chemical shift file (generated with the command CHEMS), the name of the output file, holding information on simulated peaks and for number of data points and spectral windows you wish to simulate. It generates a time domain data-set which can be subsequently processed as a regular FID.
SIN: SIN x { axis } SIN is used to multiply data by a trigonometric function varying continuously from pure sine to pure cosine. It works for 1D 2D and 3D spectra. You have to enter first the value of the parameter x varying continuously from 0 (pure cosine) to 0.5 (pure sine). x corresponds to the position of the maximum of the filter in your window. If you are working on a 2D or a 3D spectrum, there is another parameter which determines on which axis (axes) the apodization will be applies.
size: list the size parameters of the current data-set
SLOPE: slope n Will compute a relaxation rate on the current nOe build-up curve by using the initial slope method, computed from the first n points of the data-set.
SMOOTH: SMOOTH z { z2 { z3 }} where z { z2 { z3 }} is the size of the smoothing window Permits to smooth a data set by the moving-average technic. Works in 1D as well as in 2D and 3D.
SMOOTH1: SMOOTH1 n to be used with BCORR 3 controls the smoothing of data for the first segmentation 0 : no smoothing. +1 : moving average of the data set on a window of WINMA points. +10 : hysteresis smoothing of the data set with the value LEVELHYSTE.
SNAPSHOT: SNAPSHOT file_name Permits to store the current graphic display to a UIS file (VMS/VWS only) The file can then be displayed with the render command (see VWS documentation)
SPECW: SPECW x { y { z }} Permits to enter the value for the spectral width of the current data-set. One parameter will be needed for each dimension of the data-set. When reading a file the spectral width is set to 2000 * 3.1416 if no parameter block is available. The value for spectral width are changed by EXTRACT
SPIN: SPIN n Shifts the color table of 2D density image n times. Nice but probably useless. (Only VWS )
sprintf: sprintf format_string arg1 arg2 ... * realises the equivalent of a C `sprintf' all the remaining of the line up to the star is taken as arguments result is returned to the static variable $returned only one line can be put into the string, so \n cannot be used
SQSIN: SQSIN x { axis } SQSIN is used to multiply data by the square of a trigonometric function varying continuously from pure squared sine to pure squared cosine. It works for 1D 2D and 3D spectra. You have to enter first the value of the parameter x varying continuously from 0 (pure square cosine) to 0.5 (pure square sine). x corresponds to the position of the maximum of the filter in your window. If you are working on a 2D or a 3D spectrum, there is another parameter which determines on which axis (axes) the apodization will be applies.
startup.g: used as a default startup macro load the default GUI and preset some default values
STDY: Parameter for STPL. Each new line during STPL is shifted by STDY centimeters on the Y axis. Default is 0.1
STEP: Constant used when Maximum Entropy run with no line-minimization. Algo 1, (1E-6..0.5) Algo 2 or 3 (0.1 .. 10) These algorithms are usually highly inefficient.!
STEPMAX: This context holds the maximum extension of the search during the line-minimization. Default value is 1.2 for GIFA algorithm, 100 for CONJG.
STPL: STPL output This command permits to draw stacked-plots of 2D data-sets. The plot is determined by the value of the following parameters: CX : length in centimeters of a line. CY : maximum height of a peak in centimeters. SCALE : scaling applied to the data before plotting, if scale=1 then the larger peak on the surface will be CY high, if scale>1 then clipping will occur. STDY : each new line is offsetted by STDY centimeters in the Y axis. STSKIP : a line every STSKIP line will drawn. STSHIFT : each new line will shifted right by STSHIFT points, if negative then the shift is done on the left. May be fractional. STSKEW : determine how the horizontal line are skewed during plot, if negative skewed to the right, to the right if positive. output is either a file name or *s for on screen display. The command STPL? prompts you for all those parameters
STPL?: Prompts for all the parameters of the STPL command (see STPL)
STSHIFT: Parameter for STPL. STPL will shift each new by stshift points to the right during the plot. May be negative, null or positive; may be fractional. Default is 0.5.
STSKEW: Determines how the horizontal lines are skewed during a stacked plot. If 0 no skewing occurs, if positive the plot is skewed to the right, if negative, the plot is skewed to the left. For instance, a value of -1.0 will skew the horizontal by 45� to the left. STSKEW gives nice effects in conjunction with STSHIFT.
STSKIP: Parameter for STPL. STPL will skip stskip lines during the plot. Default is 1.
SUMCONS: When set to 1, the program tries to minimize the value of the sum of all the points of spectrum during the Maximum Entropy run. Should be set whenever a window 1 n is used, or when Antiphase J- deconvolution is used.
SUMREC: SUMREC x1 y1 x2 y2 Realizes the integration under a given area, value is corrected for baseline shift (if any computed with EVALN)
sumrec_1d: sumrec_1d radius_of_box integrate 1D peak on a box around each peak in the peak table
super1d: if called with no argument : builds a form which permits to superimpose up to 3 1D in the disp1d window if called with proper arguments : does actually the display
super2d: if called with no argument : builds a form which permits to superimpose up to 3 2D in the cdisp2d window if called with proper arguments : does actually the display
SVD->AR: SVD->AR n Compute the autoregressive coefficients from the singular decomposition. This is the second step of the LP-SVD method. n = 1 : forward autoregressive coefficients n = 2 : backward autoregressive coefficients n = 3 : both coefficients
SVD->DT: Compute back a new data-set from a truncated set (cf SVDCLEAN1) of singular values.
SVDCLEAN1: SVDCLEAN1 nsignals flag Keep only the first n signals singular values and put the other to 0. Use it only if you have a good insight of the number of signals in the spectrum. The flag (yes/no) determines wether you want to remove the noise power associated with the removed root.
SVDCLEAN2: SVDCLEAN2 level flag Keep only the singular values larger than level and put the other to 0. The flag (yes/no) determines wether you want to remove the noise power associated with the removed root.
SVDLIST: SVDLIST i j List the singular values from index i to j.
svd_rev: svd_rev n_of_point reconstruct the missing n_of_point first data points using the lp-svd method changes order to n_of_point*2
SWA: SWA {Fx} Consider the left part of the data as real and the right part as imaginary, and swap them to transform the data set to the internal representation of complex data; i.e. odd points real and even points imaginary. This is the opposite of USWA.
SYM: SYM n Sumetrizes the current 2D data set using either a mean value (n=1) or a smallest value (n=2) algorithm. n=3 corresponds to an algorithm which smootly switch from one algorithme to the other depending on the difference between the 2 values.

Back to Alphabetical List

SCALE

SCALE3D

SCOLOR

SEGM1

SEGM2

SET

SETPATH

SETPEAK

SETPROMPT

SETVAL

SH

SHIFT

SHOW

SHOWC

SHOWLINE

SHOWPEAK

SHOWPEAKS

SHOWTEXT

show_fit

SIGN

SIGN_PEAK

SimSpect2D

SimSpect2D_form

SIMU

SIMUN

SIMUNOE

SIN

size

SLOPE

SMOOTH

SMOOTH1

SNAPSHOT

SPECW

SPIN

sprintf

SQSIN

startup.g

STDY

STEP

STEPMAX

STPL

STPL?

STSHIFT

STSKEW

STSKIP

SUMCONS

SUMREC

sumrec_1d

super1d

super2d

SVD->AR

SVD->DT

SVDCLEAN1

SVDCLEAN2

SVDLIST

svd_rev

SWA

SYM