Version 2004 for Windows
Command Reference Guide

How to use this book

   Who should use this guide
      What FCL does
      Things to be familiar with
      Workstation requirements
   Related books
   Typographical conventions

1. Introduction

   What is FCL?
   Using this guide
   FCL command line
   Symbols and expressions
      Reserved symbols
      User symbols
   The database

2. FCL basics

   Accessing FCL
   Commands and command arguments
      Case sensitivity
      Errors in FCL commands
      Display and context effects
      Line continuation
   File prefixes and suffixes
   Macro file formats
      Comment symbols
      Tabs and spacing

3. Symbols and expressions

   Reserved symbols
      Types of reserved symbols
   User-defined symbols
      Defining symbols and their values
   Symbol substitution
      Local symbols
   Global symbols
   Arithmetic expressions
      Integer vs. real expressions
      Complex mathematical functions
      Database functions

4. Macros

   Macro directories
   Writing macros
   Executing macros
      Passing arguments to macros
   Interrupting a macro
   Loop application: Reversing a matrix
   Loop application: Accessing the database
   Branching statements
      go statements
      gto statements
      gif statements
      if statements
      if/then/else statements
      ifx statements
      exr statements
   Macro-specific commands
      com statements
      err statements
      ty and tym statements
   Using FELIX to build macros
   Some simple macro applications
      Reading files
      Plotting multiple files

5. Menus and control panels

   Menu commands
   Changing the menubar interface
      Changing the iconbar interface
   Control panels (dialog boxes)
      Types of control panel commands
      Working with control panel commands
      Output commands
      Input commands
      Control-panel dependencies
   Finding your way through menu interface files

6. Database and tables

   Structure of the database
   Database schema
      Creating database information
   Database command structure
      Basic dba subcommands
      Building database files
      Database entities
      Database items and elements
   Database item lists
      dba list subcommands
      Creating lists of information
   Spreadsheet interface

A. Command reference

   abl - Automatic baseline flattening
   abp - Automatic baseline point selection using FLATT algorithm
   abq - Automatic selection of baseline points
   abs - Absolute value replacement of work
   adb - Add work to buffer
   add - Add number to work
   aln - Antilogarithm (exponential) of work
   alt - Alternating real/imaginary
   ann - Annotate plot
   aph - Autophase spectrum
   arr - Arrow annotation
   bas - Baseline points manipulation
   bc - Baseline correct
   bck - Back-calculate NOE intensities
   bft - Bruker-Fourier transform
   bir - Read database from Insight II
   bit - Bit manipulation operators
   biw - Write database to Insight II
   bld - Build a matrix file
   bml - Get molecule name
   bun - Set bundle mode
   by, bye - Exit FELIX
   cal - Macro call
   cd - Convolution difference window
   cdf - Conditional define
   cfg - Configure memory
   cgd - Change values in the control panel
   chi - Calculate minimum chi-square value
   cl - Close a data file
   clr - Clear frame
   cls - Close output file
   cmb - Change symbol on the user interface
   cmd - List commands
   cmx - Close matrix file(s)
   cnj - Complex conjugate
   cnv - Time-domain convolution
   com - Execute FELIX commands in macros
   cp - Contour plot
   cpl - Real to complex
   csh - Circular signed shift
   csl - Circular shift left
   csp - Cubic spline baseline correction
   csr - Circular shift right
   cur - Cursor control
   dba - Database facility
   dbc - Oversampled baseline correction
   dbl - Double data size
   def - Define a symbol
   der - Derivative
   dft - Fast Fourier transform of digitally oversampled data
   dir - Current working directory
   dr - Draw work space and stack
   drb - Display brother cross peaks
   drx - Display cross peaks
   dst, exd, don, dof - Distributed processing commands
   eif - Macro end of block if
   els - Macro else block
   em - Exponential multiply
   ena - Enable multiple cursors
   end - Macro end statement
   env - Get a system environment variable
   err - Macro branch on error condition
   esc - Test for escape key event
   eva - Evaluate expression and assign to symbol
   ex - Execute a macro
   exc - Exchange real and imaginary
   exm - Execute Multiple Macros
   exp - Expanded display
   exr - Execute a macro and return
   fit - Fit 1D peaks
   flf - FaceLift baseline correction
   fli - Frequency list manipulation
   flp - Low-point fold of work space
   flt - FLATT baseline flattening
   fol - Fold work space in half
   for - Loop for macros
   fpo - Pop FELIX window
   fpu - Push FELIX window
   fra - Manipulate graphics frames
   ft - Fast Fourier transform
   ful - Full display
   fxp - Filter cross peaks
   get - Get a symbol value
   gf - Generate FID
   gif - Macro arithmetic goto
   gm - Gaussian/Lorentzian window
   gmh - Gaussian multiply in Hz
   go - Macro unconditional branch
   gre - Greek text annotation
   gto - Macro case goto
   gsp - Generate spectrum
   gv - Get value
   hav - Halve data size
   hcp - Hard copy plot
   hft - Hilbert transform
   idf - Is defined
   if - Macro if conditional branch
      Advanced if conditionals
      Macro if conditional block execution
   ift - Inverse Fourier transform
   inq - Inquire If file exists
   ins - Insight II-FELIX inter-process communication
   int - Integral
   inv - Inverse of workspace
   ip - Intensity plot
   jcp - Calculate J-coupling constant
   kw - Kaiser window
   ld - List data
   ldb - Load buffer into work space
   lim - Matrix limits
   lin - Line annotation
   lis - List symbol table
   lm - List macro
   loa - Load vector from matrix
   log - Natural logarithm of work space
   lmd - Load theoretical vector
   lpf - Linear predict first points
   lpl - Linear predict last points
   lps - Solvent suppression using linear prediction
   lpx - General linear prediction
   lrl - Find local extremum
   lvo - Load volume time course
   lwb - Load work space from bundle
   mat - Open matrix
   md - Model data
   mf - Matched filter
   mgv - Matrix get data value
   mpv-Matrix put data value
   mmp - Display memory map
   mnu - Menu manager
   ms - Magnitude spectrum
   mul - Multiply the work space by a number
   mwb - Multiply work by buffer
   nd2 - Neighbor detection in 2D NOESY spectrum
   nd3 - Neighbor detection in 3D NOESY spectrum
   nex - End of a loop
   no - Generate random noise
   nop - No operation
   nor - Normalize data
   np - Null plot
   old - Recall old limits
   opn - Open output file
   opt - FELIX option license inquiry or license checkin and checkout
   ord - Matrix dimension order
   ovc - Overlay contour plot
   pd2 - Prototype pattern detection in 2D
   pd3 - Prototype pattern detection in 3D
   pen - Define a new colored pen
   ph - Phase correction
   pic - Peak pick and label
      For 1D spectra
      For ND Spectra
   piv - Set the pivot for phase correction
   pla - Redisplay 3D object
   pol - Polynomial baseline correction
   pop - Pop the display stack
   ppm - Convert Between points and PPM
   prb - Residue type probability scoring
   prf - Formatted print
   ps - Power spectrum
   psa - Suggest assignment for a set of patterns
   psh - Push the work space onto the buffer stack
   pso - Polynomial-based solvent suppression
   puf - Formatted put
   pur - Purge symbol table
   put - Put record
   pv - Put value
   pxp - Automated peak assignment
   qsb - Skewed sinebell window
   qss - Skewed sinebell squared window
   ra - Read ASCII data
   rb - Read Bruker file
   re - Read a file (old format)
   rea - Read record from ASCII file
   rec - Rectangle annotation
   red - Reduce complex to real
   ref - Set shift reference
   ret - Macro subroutine return
   rev - Reverse
   rf - Read FELIX for Windows file
   rft - Real Fourier transform
   rj - Read JEOL file
   rm - Read macro
   rmx - Reference matrix
   rn - Read file (new format)
   rph - Real-time phase
   rpl - Real-time polynomial baseline correction
   rv - Read Varian file
   sar - Autoscreen command
   sb - Sinebell window
   sca - Scale factor for dimension
   seg - Integral segments
   sep - Separate real and imaginary
   set - Set work space to a value
   shl - Shift left
   shr - Shift right
   smo - Binomial smooth
   sp - Stack plot
   sqz - Squeeze a matrix
   srv - Set range to value
   ss - Sinebell squared window
   ssh - Signed shift
   ssp - Synthesize spectrum from peak list
   ste - Stella peak picker
   stb - Store work space to buffer
   sto - Store vector to matrix
   str - String manipulation operators
   sub - Sub-string extraction
   swb - Store work space to bundle
   sys - Execute system commands
   tex - Text annotation
   til - Tile plot
   tim - A basic clock and chronograph
   tm - Trapezoidal multiplication
   ty - Type text
   tyf - Type a file of text to the user
   tym - Type text to motif
   unf - Unfold work
   ver - FELIX version number and release date
   vol - Integrate cross peak volumes
   wa - Write an ASCII data file
   wai - Wait a while
   wm - Write macro
   wn - Write a file (new format)
   wr - Write a file (old format)
   xpa - Cross-peak assignments from shifts and spins
   xpk - Cross-peak operations
   xpl - Make a list of peaks
   xps - Generate spins and shifts from cross peaks
   xsh - Exchange stack head with work space
   xss - Simulated annealing assignment functions
   xyl - Atom list manipulation
   xyp - X,Y data pair manipulation
   xyz - Atom manipulation
   ze - Zero workspace
   zf - Zero fill
   zgt - Zero greater than
   zi - Zero imaginary
   zlt - Zero less than
   zr - Zero real
   zp - Null plot

B. Symbol reference

   absint - Absolute intensity
   absmg1, absmg2, absmg3, absmg4 - Absolute magnitude peak search window size
   animat - Animation switch
   annang - Annotation angle
   annasz - Annotation arrow size
   anncol - Annotation color
   annfil - Annotation file
   annlst - Annotation line style
   annpfx - Annotation prefix
   annsiz - Annotation text size
   annunt - Annotation units
   autox, autoy, autoz - Autorotation X-, Y-, and Z-angle increments
   autpse - Autorotation pause
   autrot - Autorotation switch
   cntrot - Autorotation count
   axsobj - Axis object switch
   axtype - 1D Axis type
   b1size, b2size, b3size, b4size - Matrix brick size
   basent - Baseline points entity
   bcfrac - Baseline correct fraction
   bckrad - Back-calculation cutoff radius
   bigpt - Big point in workspace
   blkwht - Black/White reverse switch
   button - Button status
   celpxx - Cell X pixels
   celpxy - Cell Y pixels
   center - Center plot switch
   chi - Minimum chi-square value
   clmode - Contour level mode
   cntrot - Autorotation count
   colcur - Color of cursor
   conmod - Contour spacing modifier
   contyp - Contour interpolation type
   cutoff - Cutoff for stack plot
   cycle - Color cycle length
   d1size, d2size, d3size, d4size - Matrix size
   d1vect, d2vect, d3vect, d4vect - Current vector
   datfil - 1D Data file
   datpfx - 1D Data file prefix
   datsiz - Data size
   datype - Data type
   dbafil - Database file
   dbapfx - Database file prefix
   deltax, deltay - Delta x and y for stack plot
   dimen - Number of Matrix Dimensions
   dimplt - Number of plot dimensions
   disply - Current display type
   draw3d - 3D capability switch
   drwbox - Draw box switch
   drwclv - Draw contour levels switch
   drwpks - Draw peaks switch
   drwxpk - Draw cross peaks switch
   dspmod - Display mode
   erase - Erase display switch
   etcpfx - Runtime files prefix
   first - First point
   flxver - FELIX version number
   fontsw - Font switch
   fontsz - Font size
   frsize - Frame size
   gbroad - Gaussian coefficient
   gibbs - Gibbs filter switch
   graysc - Gray scale switch
   grid - Grid switch
   gridco - Grid color
   gridst - Grid style
   hafwid - Halfwidth factor
   harddv - Hardcopy destination
   hardmo - Hardcopy mode
   hardx0, hardy0, hardxs, hardys - Hardcopy origin and size
   hfwid1, hfwid2, hfwid3, hfwid4 - Minimum peak half width
   hilim - Current plot region high limits
   hndshk - HPGL plotter handshake
   inbias, inslop - Integral bias and slope corrections
   intolp - Integral overlap
   item - Menu item
   iwidth - Interval width for baseline correction
   keyhit - Keyboard character struck
   last - Last point
   lbroad - Line broadening
   level - Contour level
   linpts - Lines/Points for draw command
   loc3x0, loc3x1, loc3y0,loc3y1, loc3z0, loc3z1 - 3D Locator endpoint coordinates
   lolim1, hilim1, lolim2, hilim2, lolim3, hilim3, lolim4,hilim4 - Current plot region low and high limits
   macfil - Macro file
   macpfx - Macro file prefix
   matfil - Matrix file
   matpfx - Matrix file prefix
   maxvol - Maximum volume slots in entity
   mdlcf1, mdlcf2 - Model data coefficients 1 and 2 (matrix factor)
   mdlpke - Model data peak entity ID
   mdlvle - Model data volume entity ID
   mdlvsl - Model data volume slot number
   menu - Menu name selected
   mframe - Matrix framesize
   minzee - Cutoff Z-magnetization for back-calculation
   mnufil - Menu file
   mnumod - Default frame position
   mnupfx - Menu file prefix
   mscale - Matrix scale factor
   msgfil - Message file
   msgpfx - Message file prefix
   msgc1, msgc2, msgi1, msgi2, msgr1, msgr2 - Character, integer, and real message parameters
   ndctyp - Normalized device coordinate type
   newhpglc - control contouring in HPGL plots
   newpostc - control contouring in PostScript plots
   nframe - Number of stack frames
   nlevel - Number of contour levels
   norval - Normalization value
   objmem - Object memory size limit
   order1, order2, order3, order4 - Matrix dimension order
   orient - Postscript orientation
   ovrlap - Stack overlap
   paphgt - Paper height
   papwid - Paper width
   pennum - Starting color
   phase0 - Zero-order phase
   phase1 - First-order phase
   picent - 1D peaks entity
   pksent - Cross peak entity
   pksobj - Peaks object switch
   pkstyl - 1D peak display style
   pkunit - Units for picking peaks
   plotd1, plotd2, plotd3, plotd4 - Plot dimension
   pltann - Annotation switch
   pltmod - Plot mode
   pltobj - Plot object switch
   pltorg - Plot origin
   pltusr - Position plot manually switch
   posneg - Negative level switch
   proj1 - Type of 1D projection onto x axis
   proj2 - Type of 1D projection onto y axis
   projct - Graphics projection type
   projsz - Size of 1D projections
   pwidth - Pen width
   redraw - Automatic backing store of plots
   refpt - Reference point
   refsh - Reference shift
   rowinc - Row increment
   scale - Plot scale factor
   schfil - Schema file
   schpfx - Schema file prefix
   segent - Integral segments entity
   segint - Segmented integral switch
   sfreq - Spectrometer frequency
   slant - Character slant angle
   smalpt - Small point in workspace
   stack - Stack depth
   status - Command status
   steang - Stereo angle
   stereo - Stereo switch
   stesep - Stereo separation
   stkord - 1D Stack display order
   swidth - Spectral width
   taucee - Correlation time
   thick - Character thickness
   thresh - Threshold for 1D peakpick
   title - Spectrum title
   tphas0, tphas1 - Total zero and first-order phase
   value - Data value
   vector - Vectors in bundle
   verify - Macro verification mode
   volent - Volume entity name
   volobj - Volume object switch
   wshift - Sinebell shift
   wskew - Sinebell skew
   x0pnt, y0pnt, x1pnt, y1pnt - Cursor position
   xangle, yangle, zangle - Euler angles
   xcells, ycells - Number of character cells
   xpixel, ypixel - Number of pixels
   xpklbl - Cross peak label switch
   xsize, ysize - Plot size
   xwalk, ywalk - Walking menu position
   xyzent - Coordinate entity
   xzero, yzero - Plot origin

C. Macro examples