This symbol controls the automatic scaling of 1D plots and 2D stack plots. By default, each plot is scaled to fill the plot area. Set absint before plotting.
dr - Draw work space and stack
This symbol controls the size of the window used to find antiphase peaks during peak picking. The search window half-width is given for each dimension to reflect the resolution of the matrix. Set absmgn before picking antiphase peaks.
This symbol controls the use of double buffered graphics for smoother display of changing plots. By default, each plot erases the frame, draws a box and axes, and then draws the spectrum. Rapid replotting causes flickering of the image. Turning on animation minimizes the flicker by not showing the new plot until it is finished.
dr - Draw work space and stack
This symbol controls the angle for displaying annotation text. All angles between 0° and 360° are allowed.
This symbol controls the size of the arrow head on annotation arrows. The size is specified in inches.
This symbol controls the color of subsequent annotations. Any valid pen number is a valid annotation color.
This symbol specifies the current annotation file. This file will be automatically drawn on the next plot whenever the symbol pltann is on, or explicitly drawn on the current plot by the ann command.
This symbol controls the line style of arrow and line annotations. Lines may be solid or dashed.
This symbol specifies the directory for reading and writing annotation files.
This symbol controls the size of annotation text. The size is in inches, and determines the height and width of each character drawn.
This symbol controls the interpretation of the position parameters for all annotation commands. Each annotation command has at least one set of x,y coordinates that define the location for that annotation. The units of these position parameters are given by this symbol, and may be any one of the choices shown below.
Normalized device coordinate units (NDC) treat any region as a range from zero to one, where the lower left corner is (x=0, y=0) and the upper right corner is (x=1, y=1).
These symbols control the autorotation of 3D plots and coordinates. Within the 3D display interface, the display can be automatically rotated for a set duration without the use of the mouse.
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Symbol Settings
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autrot
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autpse
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cntrot
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autox, autoy, autoz
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the angle in degrees to turn the display by during each step of the rotation |
projct - Graphics projection type
This symbol shows the display status of the plot axes in the 3D display interface.
This symbol controls the axis units used on 1D plots. This affects axis labeling and the units returned by the cur command.
dr - Draw work space and stack
These symbols tell the size of each brick in the current matrix. Some matrix manipulation macros can minimize the number of disk accesses by knowing the number of vectors per brick.
This is the name of the current baseline points entity.
abq - Automatic selection of baseline points
bas - Baseline points manipulation
csp - Cubic spline baseline correction
pol - Polynomial baseline correction
This symbol is not currently used.
This symbol controls which interatomic contacts contribute to the back-calculated spectrum. Only atom pairs that are closer than this distance, in angstroms, are included in the calculation.
bck - Back-calculate NOE intensities
minzee - Cutoff Z-magnetization for back-calculation
This symbol contains the largest data value of all points in the current 1D plot.
dr - Draw work space and stack
smalpt - Small point in workspace
This symbol controls the color convention used by the FELIX graphics window. The symbol must be set before the FELIX graphics window is created, and is traditionally set in the init.mac file. blkwht affects every command that draws anything on the graphics window.
This symbol contains the number of the most recently pressed button in a dialog box or database spread sheet. This allows a macro to act based on which button the user pressed. For dialog boxes, the button numbers are defined in the menu file that creates that dialog box.
dba - Database facility (dba ent edit Entity Viewer)
dba - Database facility (dba ent select Entity Selector)
These symbols contain the size of a character cell in pixels, as used by the Menu Interface. The symbols are useful for converting between pixel and character locations on the FELIX graphics window. celpxx and celpxy are set when the FELIX graphics window is first opened. The size of a character cell is based upon, and slightly larger than, the font size.
This symbol controls the centering of 1D plots.
dr - Draw work space and stack
This symbol stores the minimum chi-square value calculated by the chi command. The flt command uses this value to determine baseline segments of a spectrum.
flt - FLATT baseline flattening
This symbol controls the method used to space multiple contour levels on a plot.
dr - Draw work space and stack
conmod - Contour spacing modifier
drwclv - Draw contour levels switch
nlevel - Number of contour levels
See autox.
This symbol controls the color of all cursors used by FELIX, to the extent that the computer hardware allows. Any valid pen number is a valid cursor color. This symbol must be set before the FELIX graphics window is created. It is traditionally defined in the init.mac file. Be forewarned that the number of bitplanes in your computer and the setting of the symbol blkwht can affect the appearance of cursor colors.
This symbol controls the spacing of multiple contour levels on a plot. Each successive contour level is based on a factor of the previous level. This symbol is that factor. With linear spacing (clmode = 0) the factor is additive, while for geometric spacing (clmode = 1) the factor is multiplicative. It must have a value greater than 0.0 for clmode = 0, and greater than 1.0 for clmode = 1; the larger the value, the wider the spacing between levels.
dr - Draw work space and stack
drwclv - Draw contour levels switch
nlevel - Number of contour levels
This symbol controls the method of interpolation used when contouring.
This symbol controls the maximum peak height of stack plots by clipping off the tops of peaks that are taller than a given height. This helps to keep small peaks visible by preventing tall peaks from completely filling the plot. The cutoff height is given in inches.
cycle controls the cycling of colors when drawing multiple 1D buffers or ND contours. By default, each plot is drawn in only one color. To make multiple colored plots, increase the value of cycle to the number of different colors to use.
dr - Draw work space and stack
nlevel - Number of contour levels
These symbols contain the size in points of the current matrix, for each dimension.
dimen - Number of Matrix Dimensions
These symbols contain the indices of the vector most recently loaded out of the matrix. Note that one index is zero, denoting the dimension that the vector spans.
This symbol contains the name of the current 1D data file.
wr - Write a file (old format)
wn - Write a file (new format)
This symbol specifies the directory for reading and writing 1D data files.
datsiz specifies the size of the spectrum in the workspace, in points. This is also the size of any spectra in the buffers. The data size is used or set by virtually all the 1D commands.
lpl - Linear predict last points
This symbol defines the type of data in the work space and buffers. The data type is used or set by most of the 1D commands.
xyp - X,Y data pair manipulation
This symbol specifies the name of the current database file.
This symbol specifies the directory for reading and writing database files.
These symbols control the skew and tilt of stack plots. Valid values are in the range 1.0 to -1.0 and represent the fractional shift per data point.
This symbol contains the number of dimensions in the current matrix.
This symbol contains the number of dimensions in the current plot.
plotd1, plotd2, plotd3, plotd4 - Plot dimension
This symbol contains the type of the current plot. This is useful for knowing what kind of picture is in the current frame.
dr - Draw work space and stack
xyp - X,Y data pair manipulation
This symbol flags whether FELIX can perform 3D rotations on this computer. Note that FELIX does rotations using 3D hardware on some computers and emulates this functionality in software on other computers. This symbol is set when the FELIX graphics window first opens.
This symbol controls whether a box is drawn around plots.
dr - Draw work space and stack
xyp - X,Y data pair manipulation
This symbol controls whether contour levels are drawn on 1D plots.
dr - Draw work space and stack
This symbol controls the automatic drawing of peaks on the current plot. When on, drwpks causes the plot to automatically draw the current peaks. This is very useful for hard copy plots.
dr - Draw work space and stack
This symbol is not currently used. See drwpks - Draw peaks switch.
This symbol controls the type of data displayed in a 1D plot. By default, FELIX displays only the real components of 1D spectra.
dr - Draw work space and stack
This symbol controls whether the display is erased prior to drawing a plot. By default, FELIX clears the display before each plot is drawn.
dr - Draw work space and stack
This symbol specifies the directory for reading and writing various runtime temporary files.
This symbol controls the extent of data displayed by a 1D expanded plot. first holds the first data point to be displayed.
dr - Draw work space and stack
This symbol contains the version number of the FELIX program. flxvr is set when FELIX starts.
This symbol controls the method for generating text in PostScript hard copy plots. By default, FELIX strokes out characters using a stroke generator. This is excessively bulky and inefficient when the hard copy device has scalable fonts.
This symbol is not currently used. The font closest to the text size requested is used.
This symbol contains the maximum data size that can be held in the workspace or any buffer. This also is the maximum number of items that can be held in a database list. Reconfiguring memory is the only way to change the frame size.
nframe - Number of stack frames
This symbol determines the degree of Gaussian character that the Lorentzian/Gaussian resolution enhancement apodization function possesses. This function is intended to behave as the gm function on a Bruker spectrometer.
gm - Gaussian/Lorentzian window
Controls the Gibbs filter function of the fast Fourier transform operation. The Gibbs filter divides by two the first and last points of the data in the time domain.
bft - Bruker-Fourier transform
dft - Fast Fourier transform of digitally oversampled data
ift - Inverse Fourier transform
This symbol controls the PostScript plot output rendering. When gray scale is off, the plot is rendered in color using the FELIX pen colors. Turning gray scale on causes FELIX to render the plot in a graded gray scale.
hcp - Hard copy plot (PostScript Only)
grid controls the drawing of a grid on plots. The value of grid determines the number of grid lines or tick marks that appear for each axis label.
dr - Draw work space and stack
Sets the color to use for grids. This is usually set to 15 in mninit.mac
Sets the style of grid lines. By default, this is set to <NOBR>-1</NOBR> in mninit.mac, which produces dashed lines. If gridst is greater than or equal to zero, then straight lines are produced.
Controls the size of cross peak footprint boxes. The footprint size is twice the product of hafwid and the half-width at half-height values that are stored by the peak picker in the cross peak entity. Several commands operate on the area inside the peak footprints, so they are influenced by this symbol.
vol - Integrate cross peak volumes
This symbol is not currently used.
This symbol is not currently used.
These symbols are not currently used.
This symbol controls the peak pick command. hfwidn defines the minimum halfwidth of a valid peak, in points, for all dimensions. Any peak with less than the minimum halfwidth in any dimension is not entered into the cross peak entity.
See lolim below.
This symbol determines the handshaking values set in the HPGL hardcopy file. Setting hndshk to 0 instructs FELIX to use the handshaking values that were specified in versions 230 and earlier of FELIX. These values set software XON/XOFF handshaking with the default logical buffer size and the plotter sends XOFF to the computer when 161 free bytes remain in the plotter buffer. A more conservative handshaking scheme occurs when hndshk is set to 1. This again selects XON/XOFF handshaking but instructs the plotter to send XOFF when 1023 free bytes remain in the buffer, i.e., after one byte enters the buffer. If neither of these software handshaking choices is satisfactory, set hndshk to 3, which instructs FELIX to omit handshaking initialization commands, and create a file of the appropriate handshaking initialization instructions called pref.31 in the directory where you run FELIX. The contents of pref.31 will be appended to the beginning of the hard copy output file. Finally, setting hndshk to 2 disables software handshaking and enables hardware handshaking.
These symbols determine the amount of bias and slope correction applied to the calculation of 1D integrals. Note that accepted values are 0.0 to 1.0.
segint - Segmented integral switch
This symbol controls the extent to which drawn integrals overlap the spectrum. All values between zero and one are valid.
dr - Draw work space and stack
segint Segmented Integral Display Mode
This symbol returns the line number of the most recently selected menu on which the user clicked the left mouse button. When no item is selected, the symbol has the value 0. This symbol is set by the menu wait command.
This symbol controls noise effects in baseline correction by defining the number of baseline data values that are averaged about each baseline point to determine the baseline value used for the correction. iwidth point values above and below the baseline point are used.
csp - Cubic spline baseline correction
pol - Polynomial baseline correction
This symbol returns the keyboard character the user struck in response to any of several commands. The possible values of keyhit include: escape, mouse, motion, null, key_a...key_z, and key_0...key_2. Any command that accepts the <Esc> key to terminate that command will also set keyhit to show the termination event.
This symbol determines the last point of an expanded 1D plot.
dr - Draw work space and stack
This symbol determines the amount of line broadening, in Hertz, applied by apodization functions.
gm - Gaussian/Lorentzian window
This symbol controls the first contour level plotted. The product of the reserved symbols level and mscale determines the absolute data value of the first contour level. All matrix data points greater than that value will be plotted.
posneg - Negative level switch
This symbol controls whether the dr command displays data as isolated points, line segments or histograms. This symbol is also used by xyp to control whether x,y pairs are displayed as lines and/or points with error bars, or histograms.
dr - Draw work space and stack
xyp - X,Y data pair manipulation
These symbols are not currently used.
These symbols contain the data point limits of the current matrix plot region. In addition to reporting the current limits, they can be set by the user to affect the limits of the subsequent plot.
macfil defines the name of the current macro file.
exr - Execute a macro and return
This symbol specifies the directory for reading and writing macro files.
This symbol contains the name of the current matrix file.
This symbol specifies the directory for reading and writing matrix files.
This symbol controls the number of volume slots created when a new volume entity is built. The number of slots can not be changed once the volume entity exists. The default is six slots, and the maximum value is sixteen slots.\
These symbols contain the state of the most recent model data command. They correspond to the five parameters on the md command line.
This symbol contains the name of the most recently selected menu on which the user clicked the mouse button. When no menu is selected, the symbol has the value null. This symbol is set by the menu wait command.
This symbol controls the maximum size of matrix data files. When building a matrix, the size of the file on disk will not be allowed to exceed this size, in megabytes. Multiple disk files will be created, with the possibility of each file being on different devices.
This symbol controls the number of cross peaks generated by a back-calculation run. In theory, the potential exists to create cross peaks for all pairs of protons in the molecule. In practice, we generate only those peaks that contain more than some minimum amount of magnetization. The units are a fraction of one, with the default value being 0.001.
bck - Back-calculate NOE intensities
bckrad - Back-calculation cutoff radius
This symbol contains the name of the current menu file.
This symbol specifies that how far the frame left border should be (in characters) from the window left edge. The default is 1 character, and is set in mninit.mac.
This symbol specifies the directory for reading menu files.
This symbol controls the interpretation of what constitutes the base contour level. All data points in the current matrix that have a value greater than the product of level and mscale will be drawn by cp or ip. This symbol is not usually changed by the user.
This symbol contains the name of the most recently read message file.
This symbol specifies the directory for reading message files.
These symbols are used by the FELIX message utility to give error and warning messages to the user that contain information specific to the most recent error or warning. These symbols are not changed by the user.
This symbol controls the meaning of ndc with respect to values given to and gotten from the cursor control command. ndc treats a region as going from zero to one, with the lower left at (x=0, y=0) and the upper right at (x=1,y=1). You can set the ndc region to be either the plot box or the entire current frame.
x0pnt, y0pnt, x1pnt, y1pnt - Cursor position
If newhpglc is not set (which is the default), HPGL plots use the new contouring method. Or you can specifically set newhpglc:
If newpostc is not set (which is the default), PostScript plots use the new contouring method. Or you can specifically set newpostc:
This symbol contains the total number of 1D buffers not including the workspace. Therefore when nframe is 5, FELIX is configured for the workspace and 5 buffers.
This symbol controls the maximum number of contours drawn on a plot.
conmod - Contour spacing modifier
This symbol is not currently used. The command to normalize integral segments uses an explicit command line argument.
This symbol controls the maximum amount of memory that FELIX will use to store graphical objects. Earlier versions of FELIX were prone to crashing if all the computer memory was used. Set the object memory size limit, in bytes, before the FELIX graphics window is first created. This is usually done in the init.mac file. Setting the limit too low can impede working with objects, while setting the limit too high can allow FELIX to consume all computer memory and crash.
This symbol contains the order in which matrix dimensions will be plotted.
plotd1, plotd2, plotd3, plotd4 - Plot dimension
This symbol is not currently used.
This symbol controls the overlap of the work space and buffers when displaying a 1D plot.
dr - Draw work space and stack
stkord - 1D Stack display order
This symbol is not currently used.
This symbol is not currently used.
This symbol specifies the rendering color (i.e., the pen number) for data displays. If the pen cycle is greater than 1, the specified pen number serves as the initial color in the drawing cycle. The default pen number values are mapped to rgb colors as shown below.
On some computers, the pen number values are interpreted using modulo 7 arithmetic, that is, pennum = 8 is identical to pennum = 1.
dr - Draw work space and stack
This symbol specifies the zero-order (constant phase) parameter in degrees. Useful values range from -360 through 360 (phase0 = 180 implies that the data are to be negated).
This symbol specifies the first-order (frequency-dependent phase) parameter in degrees. The symbol value indicates the frequency dependent phase difference across the current workspace.
This symbol designates the name of the current 1D peak entity.
This symbol designates the name of the current nd peak entity.
This symbol records whether the cross peak object was enabled/disabled in the 3D real time display interface.
This symbol specifies the manner in which 1D peak extrema are marked when 1D peaks are drawn.
dr - Draw work space and stack
This symbol designates the units used to display the position of 1D peak extrema.
dr - Draw work space and stack
These symbols record the displayed orientation of ND data. The default display orientation places d1 along the x axis (horizontal: plotd1), d2 along the y axis (vertical: plotd2), and d3 along the z axis (normal to the video plane: plotd3). This orientation may be changed by the ord command and the current plot limits. The subsequently displayed orientation is recorded in the plotdn symbols. The axis orientations may thus be determined by consulting the plotdn symbols (e.g., plotd1 = 2 implies that the d2 dimension is currently displayed along the x axis, whereas plotd2 = 3 implies that the d3 dimension is currently displayed along the y axis.
dimplt - Number of plot dimensions
This symbol specifies whether or not annotations are automatically displayed on the current plot.
dr - Draw work space and stack
This symbol records the type of graphics display employed. The symbol value is determined by which version (GL or X11) of FELIX is executed, and is set when the first graphics window is opened. If FELIX is executed without graphics, the value of the symbol should be set to -1 (def pltmod -1) in the init.mac file.
This symbol records whether the data object was enabled/disabled in the 3D real-time display interface.
This symbol is not currently used.
This symbol toggles manual control over plot sizing and positioning.
dr - Draw work space and stack
This symbol specifies whether or not to display negative contour levels in 2D and 3D contour plots. Negative contours can be displayed in a different color from positive contours by setting the symbol cycle to 2.
This symbol designates the source of the 1D display projections that attend the x and y axes of a 2D plot.
projsz - Size of 1D projections
This symbol specifies the display (projection) mode.
xangle, yangle, zangle - Euler angles
This symbol designates the size of the x and y projections as a fraction of the plot sizes in their respective dimensions. Values from 0.1 to 1.0 are valid. This lets you control how much room is reserved for the projections.
proj1 - Type of 1D projection onto x axis
proj2 - Type of 1D projection onto y axis
This symbol defines the pen width in inches. This affects all axis labels, peak labels, and annotations.
This symbol enables/disables automatic storage of the contents of frames. When redraw = 1, this feature provides for a rapid recovery of the frame contents following many kinds of forced (asynchronous) redraw events (like pushing and popping the FELIX window; an exception would be resizing the FELIX window). On certain slower platforms, enabling this feature may lead to an apparent decrease in performance due to the computer's slower storage speed.
dr - Draw work space and stack
This symbol records the data point position corresponding to the reference shift value for the current contents of the workspace and all buffers.
sfreq - Spectrometer frequency
This symbol records the chemical shift value corresponding to the reference point for the current contents of the workspace and all buffers. Note that the reference chemical shift is always stored in Hertz.
sfreq - Spectrometer frequency
This symbol specifies the vector increment for stack plots and 3D contour plots. rowinc = 1 implies that every vector is drawn, whereas a rowinc = 2 implies that every other vector will be drawn. For 3D contour plots, rowinc affects the density of the "chicken-wire" mesh which constitutes the cross peak rendering. It is possible for cross peak contours to not appear if rowinc is larger that the diameter of the cross peak footprint. In both plot types, the greater the value of rowinc, the faster the plot completes (with some loss of detail).
cp - Contour plot (ND displays only)
This symbol specifies the plot scale of 1D displays and stack plots. A symbol value of 1 ensures auto-scaling of the data to fit the frame when absolute intensity mode is disabled. Scale values other than 1 apply the implied multiplicative scaling.
dr - Draw work space and stack
This symbol specifies the name of the current schema file.
This symbol specifies the directory (prefix) for reading schema files.
This symbol designates the entity in which output from the integral segments utility is stored.
This symbol defines segmented integral display attributes.
dr - Draw work space and stack
This symbol records the spectrometer frequency value for the contents of the work space and buffers.
ppm - Convert Between points and PPM
This symbol specifies the character slant angle in degrees. This affects all text including axis and peak labels, and annotations.
This symbol records the minimum data value of all points in the current 1D display.
dr - Draw work space and stack
bigpt - Big point in workspace
This symbol specifies the number of buffers displayed. A symbol value of zero implies that only the work space will be displayed, whereas a symbol value of one implies that one buffer and the work space will be displayed. The maximum value of stack is equal to nframe.
psh - Push the work space onto the buffer stack
xyp - X,Y data pair manipulation
dr - Draw work space and stack
stkord - 1D Stack display order
This symbol records whether or not a FELIX command completed without error. Many FELIX commands are capable of indicating their successful (or unsuccessful) completion using this symbol.
Error in Command...
to the parent window. It is the user's (or macro's) job to explicitly clear the status flag by entering:
def status >0
This symbol specifies the stereo angle for stereo plots in degrees. A value of 6° works well for most people. Note that this symbol's value is reset to 6° by all display commands (see below).
This symbol specifies whether (stereo = 1) or not (stereo = 0) to display a 3D object as a stereo pair.
This symbol specifies the separation between individual components of a stereo pair display of a 3D object in object point units. The symbol value is determined by the display utility, and this value will be recalculated by all display commands (see below).
This symbol designates whether the stack of buffers will be displayed with the highest numbered buffer at the top (stkord = 0) or with the lowest number buffer at the top (stkord = 1).
dr - Draw work space and stack
This symbol specifies the spectral width in Hertz. Note that this symbol is set by the re and rn commands using the value in the data file header.
gm - Gaussian/Lorentzian window
ppm - Convert Between points and PPM
sfreq - Spectrometer frequency
This symbol specifies the correlational time in nanoseconds (that is, the time it takes a molecule to rotate one radian) and is used to conduct back-calculation simulations.
bck - Back-calculate NOE intensities
This symbol specifies the number of "restrokes" for pen plotters. A symbol value of 0 implies a single stroke. This affects all text, including axis and peak labels.
This symbol specifies the threshold data value for picking 1D extrema. Any peaks with heights below this threshold are not picked.
This symbol designates a plot title, but is not currently used.
These symbols are not currently used.
This symbol is not currently used.
This symbol contains the total number of vectors along the specified dimension of the matrix. The bundle mode command sets the value of vector.
This symbol controls the diagnostic monitoring of macro execution. This is useful for debugging macros, or for tracing the flow of macro and menu file calls. All output generated goes to the output window..
This symbol contains the name of the current volume entity. The volumes calculated by the vol command are stored in volent.
vol - Integrate cross peak volumes
This symbol is not currently used.
This symbol is not currently used.
This symbol is not currently used.
These symbols interact with the locator device using the cur command. The symbols are used to set the cursor position when pre-positioning the cursor, and to return the cursor position when the cur command is completed. The units for the cursor position in both cases depend upon the map argument given to the cur command. Cur commands that return a single point place the cursor position values in x0pnt and y0pnt. Commands that return a pair of points fill x1pnt and y1pnt too.
The mnu wait command sets the values of x0pnt and y0pnt to the pixel values of the cursor position when the menu item is selected.
pic ND Peakpick (pick modes 4 and 5 only)
These symbols contain the angle of rotation about the x, y, and z axes applied to the matrix displayed by the 3D display interface. The angles are given in units of degrees.
When projct = 3, these angles control the projection of 3D plots onto the 2D display surface.
These symbols provide the width and height of the current FELIX window in character cells. These are the units for menus and dialog boxes. The symbols are set by FELIX when the window is created or resized.
These symbols provide the FELIX window size in pixels. These are set by the user in the init.mac file at startup to define the initial size of the FELIX window. Thereafter, using the window manager widgets to resize the FELIX window updates these symbols.
This symbol controls the display of cross peak labels in 2D and ND plots.
These symbols control the size of the next plot, or contain the size of the current plot, depending on the value of pltusr. Sizes are in inches.
dr - Draw work space and stack
pltusr - Position plot manually switch
These symbols return a position near the cursor in character cell units when the user clicks the mouse button on a menu selection. The position represents the best location to place the next menu to create the appearance of walking menus.
This symbol contains the name of the current atom coordinate entity.
bck - Back-calculate NOE intensities
These symbols control the origin of the current plot relative to the origin of the current graphics frame or plot device.
dr - Draw work space and stack
See x0pnt, y0pnt, x1pnt, y1pnt - Cursor position.
See x0pnt, y0pnt, x1pnt, y1pnt - Cursor position.
See xangle, yangle, zangle - Euler angles.
See xcells, ycells - Number of character cells.
See xpixel, ypixel - Number of pixels.
Seexwalk, ywalk - Walking menu position.
See xzero, yzero - Plot origin.
See xangle, yangle, zangle - Euler angles.
All symbols listed in this appendix are reserved symbols.