The abl command first determines whether each point in the work space is baseline or not. abl then goes through all points, convolving baseline points with a moving average and applying a straight-line correction to non-baseline intervals. This algorithm was developed by W. Massefski.
abl is very robust and requires as input only estimates of the point-wise half width of the widest spectral line and the desired convolution width for noise. This algorithm has the unusual characteristic of not only flattening the baseline, but convolution of baseline intervals actually reduces the noise level. abl does an excellent job on sparsely populated spectra such as slices of multidimensional data that contain mostly baseline. For reliable operation, line points should be set much larger than noise points, otherwise abl may interpret the tails of peaks as noise and bite chunks out of them.
Since abl selects unique baseline points for each spectrum, it is not necessary to define a list of baseline points, nor are the points used saved in the baseline entity.
See also:
flf FaceLift baseline correction
abp uses the FLATT algorithm (Güntert, 1992) for selecting baseline points in a spectrum. The resulting points are stored in the entity whose name is stored in the basent symbol. Before running the abp command, you may decide to run the chi command: the value returned by the chi command is stored in the chi symbol and is read automatically by abp.
abp begins by calculating the chi-square value for a fit of (2*baseline_width + 1) data values to a straight line at points (1 + baseline_width) to (npoint - baseline_width).
The command works by comparing the minimum chi-square value in an interval of (baseline_width * 2/3) that is centered on point (baseline_width/3 + 1). If the minimum chi-square value is less than (tau * chi), the central point is stored in the baseline point entity. The comparison is repeated every stride points.
Symbol dependence
chi Minimum chi-square value
See also
chi Calculate minimum chi-square value
flt FLATT baseline flattening
flf FaceLift baseline correction
abq selects baseline points of the data in the work space automatically, and places the resulting points in a database entity defined by the symbol basent. If no parameters are entered, abq uses defaults that work well for most spectra. First, abq divides the data in the work space into segments of interval size in points. For each segment, it calculates the mean data value of the points and the deviation of each point from the mean. Next, it collects the largest deviation value, which is called the segment deviation, from each segment and orders them from smallest to largest. Finally, any segment with a segment deviation that is less than a cutoff value is to determined to be baseline. The cutoff value is calculated as the product of standard deviation and the smallest segment deviation value. The bas command can be used to add or delete baseline points in the baseline entity.
Following abq, a polynomial or cubic spline baseline correction may be executed using either polynomial baseline correction (pol) or cubic spline baseline correction (csp).
basent Defines Baseline Points Entity
See also
csp Cubic Spline Baseline Correction
flf FaceLift baseline correction
pol Polynomial Baseline Correction
bas Baseline Point Selection
abs replaces each point in the workspace with its absolute value, i.e.:
abs should not be confused with ms, which calculates the absolute magnitude of complex points.
Symbol dependence
datsiz Number of Data Points
See also
ms Magnitude Spectrum
ps Power Spectrum
adb adds the data in the work space to the specified buffer. This command is very useful for saving intermediate results or for generating projections of multidimensional spectra.
Symbol dependence
datsiz Number of Data Points
datype Data Type
See also
ldb Load Buffer to Workspace
mwb Multiply Work by Buffer
stb Store Workspace to Buffer
add simply adds the specified number value to each data point in the work space.
Symbol dependence
datsiz Number of Data Points
datype Data Type
See also
mul Multiply Work Space by a Number
aln replaces each data value of the workspace with e(work), its natural (base e) antilogarithm or exponential. The aln command is the inverse of the logarithm of workspace (log) command.
Symbol dependence
datsiz Number of Data Points
See also
log Logarithm of Workspace
alt changes data consisting of separate real and imaginary parts to alternating real and imaginary parts. All complex data within FELIX is processed in the alternating mode. The alt command is thus useful for restoring imaginary parts of N-dimensional hyper-complex spectra (separated using sep) for phasing after transformation. alt defines the data type to be complex (datype=1) and sets the data size (datsiz) to half the original number of real points.
Symbol dependence
datsiz Number of Data Points
datype Data Type
Symbol Changed
datype Data Type
See also
sep Separate Real/Imaginary
ann annotates the current plot according to the contents of the file designated by the symbol annfil. The annotation file contains annotation commands. To annotate hardcopy plots, simply define the symbol pltann to 1 before issuing the hcp command.
Symbol dependence
annfil Annotation File
annpfx Annotation Prefix
See also
arr Arrow Annotation
lin Line Annotation
tex Text Annotation
gre Greek Annotation
rec Rectangle Annotation
aph provides functions for automatic phase correction for 1D and ND spectra. For details see Chapter 8, Theory, in the FELIX User Guide. Used without subcommands, aph calculates the phase error and corrects the spectrum displayed in the workspace. It is sensitive to several factors, including bad baselines. Autophasing a spectrum that has a large amount of baseline roll does not yield a well phased spectrum. aph by itself is recommended for proton spectra. It does not use the excluded areas as it does when subcommands are included.
aph zero removes all defined excluded areas.
aph exclude adds an excluded area that is ignored while computing the phase parameters using the aph cal subcommand. Any datapoints falling between minpt and maxpt along dimension dim are ignored. An excluded area is usually a solvent region. Up to 10 excluded areas can be defined. If dim, minpt, and maxpt are not specified, aph exclude displays the currently defined excluded areas.
aph calculate calculates the zero and first-order phase parameters for a 1D spectrum in the workspace or for a certain dimension of the current 2D or 3D spectrum. It does not change the spectrum.
Symbols changed
phase0 Zero order phase correction
phase1 First order phase correction
See also
ph Phase spectrum
rph Real-time phase
arr draws an arrow on the current plot with its tail at the (X0,Y0) point and its head at the (X1,Y1) point. The optional coordinates are useful if the matrix is a 3D or 4D and the current plot is a strip plot. The arrow should be drawn starting in one strip and ending in another strip, where the strips are taken from different slices of the ND matrix. All arrow coordinates are interpreted based on the symbol annunt according to the following table:
The color of the line is determined by the symbol anncol, the style of the line (solid or dashed) is defined by annlst and size of the arrowhead is determined by the symbol annasz.
Symbol dependence
anncol Annotation Color
annasz Arrowhead Size
annlst Annotation Line Style
annunt Annotation Units
See also
ann Annotate Plot
lin Line Annotation
bas provides the ability to assemble and display the array of points that are required for baseline correction. The entire array of points may be selected interactively, or alternatively, baseline points may be selected automatically using abq, and additional points may be added manually. The x-axis point value specifies the data point to add to the baseline points database entity (by default, bas:baseline). A parameter value of -1 for add enables a crosshair cursor for point selection. The entire array of baseline points may be discarded by invoking bas zero.
The baseline points manipulation operators and their parameters are as follows:
Symbol dependence
basent Baseline Entity
See also
abq Automatic Selection of Baseline Points
csp Cubic Spline Baseline Correction
flf FaceLift baseline correction
pol Polynomial Baseline Correction
bc removes a DC offset of the FID baseline (DC offset creates a spike at the carrier frequency) by subtracting the offset from work. bc will work properly only if the data at the end of the FID is a baseline. Adequate DC offset correction is usually obtained by using the default fraction value of 0.25, although, for FTIR, fraction is set to 1.0, and bc is computed on the entire contents of the work space, as there is no intensity at zero frequency.
Symbol dependence:
datsiz Number of Data Points
bck -- Back-calculate NOE intensities
bck calculates expected NOE cross peak intensities from the structure in the entity xyz:atoms. Chemical shifts and line widths are extracted from the shift entity, and a cross peak entity bckxpk and corresponding volume entity bckvol are built. The volumes are calculated for the specified mixing time mix in seconds. The rleak parameter specifies the leakage rate of Z-magnetization over time and is in sec-1 units. The cross-relaxation rate is determined by the symbol taucee in ns units. The symbol bckrad allows you to save time by ignoring spin pairs further apart than bckrad Å. This algorithm generates NOE intensity by using matrix doubling at a spectrometer frequency spcfrq in MHz units. The symbol minzee is used to filter out interactions below some sensible threshold that would not be observed experimentally. There is an upper limit of 2048 spins for the simulation.
There is another form of this command which can be used in conjunction with the Assign module:
Once you have a spectrum_id spectrum defined in the Assign database, FELIX calculates the theoretical spectrum using all the information in the database (e.g., assigned patterns, assigned peaks, mixing times, transfer types, and spectrometer frequencies). That also means that if the spectrum specified is a 3D NOE-NOE, then FELIX will back-calculate a 3D NOE-NOE theoretical spectrum.
The theory behind bck is described in the Chapter 2, Theory, in the FELIX User Guide. It will efficiently generate expected spectra, and is very useful when generating structures from NOE data.
taucee Correlation Time (ns)
bckrad Back-Calculation Radius (Å)
minzee Minimum Z-Magnetization
spcfrq Spectrometer Frequency (MHz)
bft transforms a Bruker FID in the workspace into a frequency-domain spectrum. Many Bruker spectrometers acquire real and imaginary data at alternate points in time rather than simultaneously, resulting in rolling baselines and phase errors. Modern Bruker spectrometers are capable of true quadrature, and we recommend that you use this acquisition mode if possible.
Symbol dependence
datsiz Number of Data Points
datype Data Type
See also
ft Fourier Transform
rft Real Fourier Transform
ift Inverse Fourier Transform
This set of commands allows you to read NMR Refine database files from the disk.
bir pks reads an Insight II peak file into the current peak entity (table).
bir asn reads an Insight II peak assignment file into the current peak entity (table).
bir ppm reads an Insight II resonance assignment file into the current pattern entity (table).
bir rstrnt reads an Insight II restraint file into the current restraint entities (tables).
Symbol dependence
pksent Current peak table
volent Current volume table
rpaent Current pattern table
rreent Current resonance table
See also
ins Insight-FELIX Inter-Process Communication
biw Write Database to Insight II/NMRRefine
The bit clear command clears a bit in the mask to zero. If bit is less than one, all bits in the mask are zeroed. The new bit mask is returned in symbol.
The bit set command sets a bit in the mask to one. If bit is less than one, all bits in the mask are set to one. The new bit mask is returned in symbol.
The bit test command tests a bit in the mask. The value of that bit (zero or one) is returned in symbol.
The bit or command combines two bit masks using the logical "or". The new bit mask is returned in symbol.
The bit and command combines two bit masks using the logical "and". The new bit mask is returned in symbol.
The bit xor command combines two bit masks using the logical "xor". The new bit mask is returned in symbol.
The bit not command reverses all the bits in a mask. The new bit mask is returned in symbol.
The following parameters are used with the bit commands:
This set of commands allows you to write NMR Refine database files to the disk.
biw pks writes an Insight II peak file to the disk using the current peak entity (table).
biw asn writes an Insight II peak assignment file to the disk using the assignments in the current peak entity (table).
biw ppm writes an Insight II resonance assignment file to the file using the current pattern entity (table).
biw rstrnt writes restraint file to the disk using the current restraint entities (tables).
Symbol Dependencies
pksent Current peak table (needed for biw asn and biw pks)
volent Current volume table (needed for biw asn and biw pks)
rpaent Current pattern table (needed for biw ppm)
rreent Current resonance table (needed for biw ppm)
noerst Current NOE-distance restraint table
noeors Current NOE-overlapped distance or ambigous distance restraints
dihrst Current dihedral restraint table
mixrst Current mixing time table
volrst Current NOE-volume restraint table
volors Current NOE-volume overlapped or ambiguous intensity restraints
rchrst Current remote-chiral restraint table
chirst Current chiral restraint table
j3drst Current 3J-dihedral restraint table
ndirst Current NMR dihedral restraint table
disrst Current distance restraint table
See also
ins Insight-FELIX Inter-Process Communication
bir Write Database to Insight II/NMR Refine
In the following example, a three-dimensional matrix called test.mat, 512 ¥ 256 ¥ 32 points, is created.
bld creates a file, or a series of files, to contain an N-dimensional matrix. The size of the matrix is restricted to powers of two in each dimension, with a minimum size of 4 points. If a matrix is defined with a size that is not a power of two, bld will use the next highest power of two. FELIX matrices exist as direct-access files on disk, and may exist as multiple files if desired. The maximum file size of the matrix is defined using the matrix frame size symbol (mframe). When the actual size of a matrix exceeds mframe megabytes, multiple files will be created. Once a matrix has been built using bld, you open it using the command mat to access vectors, planes, and other subspaces.
Symbol dependence
matpfx Matrix Prefix
mframe Matrix Frame Size
bml clears up the molecule buffer and sets up the molecule name. This is needed if the molecule is displayed in Insight II.
Symbol changed
bmlname Molecule Name
See also
ins Insight-FELIX Inter-Process Communication
bir Read Database from Insight II/NMR Refine
biw Write Database to Insight II/NMR Refine
bun defines a matrix dimension for bundle mode operation. bun also defines the value of the reserved symbol vector as the total number of vectors along the specified dimension in the matrix. For example, for a 512 x 256 x 32 matrix, you have to perform 512 x 256 operations when transforming the third dimension, therefore vector is calculated to be 131072 (= 512 times 256). In this example, with bun 3, successive vectors are loaded into the work space from the matrix using the load work space from bundle command (lwb), operated on (apodized, Fourier transformed, and phased) and stored back to the matrix using the store work space to bundle command (swb). Following the last lwb or swb access, the bun 0 command is issued to terminate bundle mode access and to return to discrete access mode.
Bundle mode is very useful for processing all vectors along a single dimension of a matrix in exactly the same way when the order of processing does not matter. For example, when processing the third dimension of a 3D experiment, it does not matter which D3 vector is transformed first, only that it is transformed once during the processing. A matrix transformation performed in bundle mode is many times faster than the same transformation performed in discrete vector mode. To exit bundle mode and enter discrete vector mode, enter bun 0.
At any one time, a matrix must be either in bundle mode or in discrete vector mode (the default). When in bundle mode, the load command (loa) and store command (sto) cannot be used to access discrete vectors in the matrix. Likewise, when in discrete vector mode, the bundle mode commands lwb and swb cannot be used.
Symbol changed
vector Number of Vectors in the Entire Bundle
See also
lwb Load Work From Bundle
swb Store Work to Bundle
bye ends the session with FELIX and returns you to the operating system. Any open matrices are closed. If a database is in use, you will be prompted to save or discard changes for this session.
cal performs a subroutine call within a macro. The called macro is read into the macro work space and given a label of $macroname. Control is transferred to the first line of the called macro, and the macro executes until complete. Control then returns to the line following the cal command. The called macro remains in the macro work space until another macro is executed, so repeated calls will be efficient. cal is only valid in a macro.
See also
exr Execute Macro and Return
ret Macro Subroutine Return
cd -- Convolution difference window
cd is an apodization function, which is really a special case of convolution difference, namely, the difference between no line broadening and lbroad. The cd command uses the global symbol lbroad if no line broadening parameter is entered. cd multiplies each point in the work space by the function:
cdf lets you define a symbol to have a value, only on the condition that the symbol is not yet defined.This is a good way to guarantee that a symbol has a value without changing the value if it already exists. Since it is an error to use an undefined symbol, this command can simplify writing robust macros.
cfg allows you to reserve memory for 1D work spaces. When configuring memory, a good rule of thumb is to set the 1D work space size to the maximum size data you plan to work with, and then set the count parameter to the maximum number of buffers you need plus one. If you need access to more than one buffer, simply set count to a larger value (the maximum value is 64). However, by setting count to a larger value (thus, allocating precious memory to 1D work space), you may be unable to open a multidimensional matrix (matrices also need memory). In this case, it may be necessary to reduce the size of the 1D work space and buffer memory with the cfg command.
You may notice that using the cfg command while a matrix is open will close the matrix before reallocating the 1D workspaces. After configuration, you must open the matrix again to access it.
Symbol changed
frsize Workspace and Buffer Size
nframe Number Of 1d Buffers
See also
mmp Memory Allocation Map
cgd updates symbols on a non-modal (mnu a) control panel.
For the spectrum in the work space, chi calculates a minimum chi-square value, which is stored in the symbol chi and used by the flt command. This minimum chi-square value is calculated by fitting the data values within a window of baseline_width length to a straight line, and calculating the chi-square value for the fit. The chi-square value is calculated for each full window of data values, as the window is moved point-by-point along the spectrum. The smallest chi-square value is stored in chi.
Symbol Changed
chi Minimum Chi-Square Value
cl closes the current data file being accessed by FELIX. A subsequent read command (re or rn) reads the first record of the data file.
See also
re Read Data File (Old Format)
rn Read Data File (New Format)
wr Write Data File (Old Format)
wn Write Data File (New Format)
clr causes the current graphics frame to be erased. The frame will no longer have any current graphics context or mapping.
Symbol changed:
disply Current Frame Display
cls closes the current output file. Unless an output file is open, the put record command (put) will take no action.
See also
put Put Record
opn Open Output File
This command changes the text in the FELIX user interface, where an item was defined via the symbol.
This command causes FELIX to list all commands. If a match string is entered, only commands that match the string will be listed.
cmx closes all open matrix files. The matrix buffer is also de-allocated.
Symbol changed
matfil Current Matrix File
dimen Number of Matrix Dimensions
See also
bld Build Matrix
mat Open Matrix
cnj negates the imaginary part of the data in the workspace. This command will reflect the spectrum about zero frequency if it is performed before the ft.
Symbol dependence:
datsiz Number of Data Points
datype Data Type
cnv is used to eliminate huge solvent lines and the effect of the tails of these lines on less intense signals. cnv convolves the FID with the selected window of the specified width, then subtracts the result from the original FID. Lines are removed only within a small range of zero frequency, and the effective width of the range is dependent on the window size used, that is, the wider the window, the narrower the width of the range. Convolution of finite length data sets necessarily begins at the point
window_size and ends at the point (datsiz -- window_size). Therefore, another method for estimating the solvent signal must be used to for the first and last
window_size points. The extrapolation parameter allows you to select either a linear extrapolation, which is fast and usually sufficient, or a linear prediction estimation, which is slow but often more accurate. The linear prediction can produce undesirable results under certain conditions; for example, when the window_size is narrow, the convolved data possesses higher frequency components that the linear prediction subsequently attempts to extrapolate. For extrapolation of one, the linear prediction parameters are points = 32, coefficients = 16, and peaks = 8. This technique was developed by Dominique Marion.
Symbol dependence:
datsiz Number of Data Points
datype Data Type
See also:
lpx General Linear Prediction
lpf Liner Predict First Point
lbl Linear Predict Last Points
com puts you in touch with the command interpreter of FELIX while a macro is running. This allows you to input a FELIX command while a macro is running. The command is then executed within the macro. The string must be a valid FELIX command line. com is only valid in a macro.
cp draws a contour plot of the current plot region, defined by the matrix limits command (lim) on the current graphics device. The lowest contour level is determined by the product of the reserved symbols level and mscale.
The contouring algorithm can perform spline interpolation (contyp=1) between the real points, making the appearance of the plot smoother. While this improves the appearance, the speed of the plotting decreases.
The default rendering mode erases the screen before each display; this action may be disabled by setting the reserved symbol erase to 1. Video buffering may be enabled by setting the reserved symbol animat to 1. The size and graphics attributes of the region plotted by the cp command are affected by a number of other reserved symbols.
Symbol dependence:
animat Specifies Video-Buffering
clmode Selects Linear or Geometric Contour Spacing
conmod Modifies Contour Level
contyp Interpolation Type
cycle Sets Color Cycle
drwbox Draws Box Around Plot
drwpks Draws Peaks Switch
erase Disables(0)/Enables(1) Automatic Screen Erasing
grid Specifies Superimposed Grid Lines
level First Contour Level
mscale Matrix Scale Factor
nlevel Number of Contour Levels
posneg Enables Plotting of Negative Contour Levels
projct Selects Dimensionality of Display
pennum First Color
rowinc Point Skipping Factor for 3D Displays
xpklbl Label Peaks Switch
Symbol changed
disply Current Display Type
See also
ip Intensity Plot
np Null Plot
sp Stack Plot
ovc Overlay Plot
pla Fast Replot of 3D Object
rmx Reference Matrix (Sets Axis Type)
cpl turns a real vector into a complex vector with an imaginary part of zero. This command works only on data stored in the current workspace.
Symbol dependence
datsiz Number of Data Points
datype Data Type
Symbol changed
datype Data Type
See also
red Reduce Complex to Real
csh shifts the data in the work space left or right the number of points specified by the value [(n1-n2)*scale]. Negative shifts move to the left, positive shifts move to the right. Points shifted off the leading edge of the spectrum are "circular shifted" to the trailing edge. The csh command is used for tilting spectra where the scale is usually set to the digital resolution ratio of the 1 and 2 dimensions.
Symbol dependence
datsiz Number of Data Points
datype Data Type
See also
shl Shift Left
shr Shift Right
ssh Signed Shift
csr Circular Shift Right
csl Circular Shift Left
csl shifts the data in the work space left by the number of points specified. Points shifted off the left edge of the spectrum are circular shifted back onto the right edge of the spectrum.
Symbol dependence
datsiz Number of Data Points
datype Data Type
See also
csr Circular Shift Right
ssh Signed Shift
csh Circular Signed Shift
shl Shift Left
shr Shift Right
csp performs a cubic spline baseline correction on the contents of the workspace according to the baseline points defined in the baseline entity basent. The baseline points may be set automatically using the automatic selection of baseline points command (abq). csp uses the value of the interval width symbol (iwidth) to minimize the effects of noise on the correction by averaging the points within the interval about each baseline point plus and minus the value of iwidth.
A cubic spline will correct each baseline point to exactly zero. This can present a problem if csp is used to correct the first dimension of a multidimensional transform. Since each defined baseline point will be corrected to zero, the transform along the next dimension will see all zeroes when the vector passing through the baseline point is loaded. The FFT of all zeroes is all zeroes, and if a DC offset is present in the data, this will appear as ridges or valleys in the transformed data. We recommend pol for baseline correction during transforms.
Symbol dependence
datsiz Number of Data Points
datype Data Type
iwidth Interval Width
See also
abq Automatic Selection of Baseline Points
flf FaceLift baseline correction
pol Polynomial Baseline Correction
bas Baseline Point Manipulation
csr shifts the data in the work space right by the number of points specified. Points shifted off the right edge of the spectrum are circular shifted back onto the left edge of the spectrum.
Symbol dependence
datsiz Number of Data Points
datype Data Type
See also
csl Circular Shift Left
ssh Signed Shift
csh Circular Signed Shift
shl Shift Left
shr Shift Right
cur allows you to control the cursor location and appearance, wait for mouse or keyboard events, and obtain positional information from the graphics display.
The general outline of the behavior of the cur command is:
1. Change the cursor to a particular style, and optionally preposition it at a specified position on the graphics display.
2. Wait for zero, one, or two mouse button or keyboard events.
3. Return positional (x, y location) and event (key or mouse button) information from the cursor into reserved symbols for future use.
4. Change the cursor to a particular style on exit. There are many variations of the cur command, with the specific behavior determined by the parameter values. General descriptions of each parameter are given below:
* exit_style is not used with stationary cursor
** multiple cursors always return axis units
Symbol dependence
ndctyp Normalized Coordinate Type
x0pnt First X Position
y0pnt First Y Position
x1pnt Second X Position
y1pnt Second Y Position
Symbol changed
keyhit Cursor Key Event Code
x0pnt First X Position
y0pnt First Y Position
x1pnt Second X Position
y1pnt Second Y Position
See also
ena Enable Multiple Cursors
dba provides access to a database that can be used to store spectral features and relational information. The database is a central part of FELIX, and Chapter 7, The Database, contains detailed information on all aspects of its use.
oversampled decimation factor |
dbc removes a DC offset of a digitally oversampled Bruker FID baseline (DC offset creates a spike at the carrier frequency) by subtracting the offset from work. The dbc command works properly only if the data at the end of the FID is a baseline. Adequate DC offset correction is usually obtained by using the default fraction value of 0.25.
Symbol dependence
datsiz Number of Data Points
dbl doubles the size of the data in the workspace by performing a linear interpolation between the existing data points.
Symbol dependence
datsiz Number of Data Points
datype Data Type
Symbol changed
datsiz Number of Data Points
def is used to explicitly define values for specified symbols. These defined symbols can then be used in macros in the form of &symbol. When the &symbol notation is encountered within a macro, the symbol's value replaces the symbol's name before command execution.
In this example, the symbol count is given an explicit number value of 10. Subsequently, if you run a macro containing the following command:
the explicit number value of count replaces the symbol. In this example, the for loop increments 10 times as defined by the value of the symbol count.
There are two classes of symbols within FELIX, namely reserved symbols and user symbols. Reserved symbols have pre-defined meanings in FELIX, whereas user symbols have no pre-defined names or meanings. For a complete list of the reserved symbols and their meanings, see Appendix B, Symbol Reference.
Symbol changed
Only the symbol named in the def command
See also
lis List Symbol Table
get Get Symbol Value
eva Evaluate Expression
pur Purge Symbols
der takes the derivative of the data in the workspace and pushes it onto the current buffer stack. The workspace is left unchanged.
Symbol changed
stack Stack Depth
dft performs a complex fast Fourier transform on a digitally oversampled Bruker FID in the work. It uses the optional decimation_factor and version variables to use the correct algorithm. Alternatively, you can omit these two variables but you must set the decim and dspfvs symbols. The symbols correspond to the BRUKER parameters DECIM and DSPFVS, respectively.
The currently supported versions (dspfvs) are 10, 11, and 12. If there will be a newer version then you can enter the 21 phase parameters into FELIX through an ASCII file, which is then read by FELIX when it executes the dft command. The file is located in the $BIOSYM/macros/felix directory and should be called according to the version number:
The dft command executes more quickly if the size of the data in the workspace is a power of two, but it will transform data of any size.
If the symbol gibbs is set to 1, the first point of the workspace is divided by two before transformation to properly weight the time period this sample represent. If gibbs is set to zero, the division is not performed.
Symbol dependence
datsiz Number of Data Points
decim Decimation factor (from BRUKER DECIM variable in acqus)
dspfvs Oversampling version (from BRUKER DSPFVS variable in acqus)
gibbs Gibbs Filter Switch
See also
rft Real Fourier Transform
bft Bruker-Fourier Transform
ift Inverse Fourier Transform
dr draws the contents of the workspace (default) as well as the number of buffers indicated by the stack depth symbol stack.
Symbol dependence
absint Absolute Intensity
animat Enable Double Buffering
axtype Axis Type
center Center Zero Switch
cycle Color Cycle
drwbox Draw Box Around Plot
drwclv Draw Contour Levels
drwpks Show Picked Peaks
dspmod Display Mode
first First Point
last Last Point
linpts Line/Points Switch
ovrlap Plot Overlap
pennum Starting Color
pltann Plot Annotations
scale Scale Factor
segint Show Integral
stack Stack Depth
Symbol changed
smalpt Smallest Data Value
bigpt Largest Data Value
disply Current Display Type
See also
exp Expand Plot
ful Full Plot
old Old Plot Limits
drb draws lines that connect cross peaks having the same parent. drb uses the parent pointer element of cross peaks to determine whether two cross peaks are brothers. The peaks parameter can specify either a DBA entity name or a DBA list number.
See also
drx Draw Cross Peaks
xpl Cross Peak List Manipulation
drx displays cross peaks in the database that are in the current plot region on the current display. If the display is 2D, 2D cross peaks will be displayed. In 3D mode, cross peaks will be displayed as 3D objects. The peak entity can specify either a DBA list number or DBA entity name.
If the color is defined as -1, then the peaks in a 2D plane of a 3D or 4D matrix are colored depending on the relative positions to the current plane. Defining color as -2 colors peaks based on assignment states, and -3 colors the peak boxes based on whether or not they belong to prototype patterns within Assign. If color is defined as -4, then the peak set of a different matrix (matfil) will be displayed on the current matrix with color = overlaycolor.
The relative dimensions (i.e., what dimension of the peak set should be displayed on what dimension of the spectrum) is defined with the repek1, repek2, ... user symbols.
Example: to display an HSQC peak set (D1 = HN, D2 = N-15) on a HSQC-NOESY spectrum (D1 = HN, D2 = H-1, D3 = N-15) set the following variables:
Symbol dependence:
xpksym Peak Symbol Switch
xpklbl Label Peaks Switch
A macro can be distributed through several machines by creating a top level macro which contains a command(s) directing FELIX to use the given machines for distributed processing, preferably at the very beginning of the macro.For example:
Note that the matrix to be processed should be seen from the computers where the distributed processing will be happening (through NFS).
This command can be run on multiprocessor SGI's in distributed parallel mode -- that is, each processor runs its own copy of FELIX.This top level command calls the macro to distribute using the command:
This executes a macro in distributed mode and then returns to the current macro, continuing with the line immediately following this exd command. The called macro is deleted once it completes, and the current calling macro is not disturbed.
The macro for distributed processing should contain a command from which to start the distributed processing:
The macro after the don command should contain processing instructions using the bundle mode.
At the very end of the macro before the return statement (ret and end) there should be a command to finish the distributed processing:
Executing this macro results in distributing the bundles along that dimension through the machines defined by the dst command, while the original FELIX process returns to the calling macro or prompt. Certainly you can set the current machine as one of the target machines or even as the only target machine (which is effectively the background processing), but that is a separate FELIX process.
eif defines the end of a block-form macro if statement. See the if documentation for a complete description of the if/else syntax.
els defines the beginning of the else portion of an if/else statement. See the if documentation for a complete description of the if/else syntax.
em multiplies the data in the work space by an exponential window. This apodization function is used to reduce noise at the expense of spectral resolution. The parameter line broadening may be entered with this command or, if no line broadening parameter is specified, the current value of the line broadening symbol (lbroad) is used. It is important that the swidth parameter is set correctly otherwise the window function will be improper.
Symbol dependence:
datsiz Number of Data Points
datype Data Type
lbroad Line Broadening
swidth Spectral Width in Hz
ena enables a correlated cursor in a single frame, based on the current graphics context from the current plot. If multiple frames have correlated cursors enabled, the cur command can be used to enable correlated cursors that appear in all enabled frames in corresponding axis unit positions. Any new graphics display in a frame with a correlated cursor enabled will automatically disable the correlated cursor since the display context changed.
end terminates macro execution and returns to command mode. end is only valid in macros.
env allows the user to read the UNIX environment variables from inside FELIX. If env_var exists in the current process's environment, then symbol receives the value of that environment variable. If the environment variable does not exist, the symbol is left unchanged.
err defines an error trap response for a macro. Once an err command has been executed by a macro, any subsequent error condition will cause a branch to the specified macro label, or execution of the specified macro. The err destination is valid for the duration of the macro. err is only valid in macros.
symbol to receive escape event status: 0=escape key has not been pressed, 1=escape key has been pressed |
The esc command lets you watch for an interrupt request inside a macro. When placed in a macro for loop esc can be used as a way to exit the processing macro before normal completion.
Be warned that there are several commands that also intercept escape key events, and may deal with the escape event before the esc command is encountered during macro execution. These commands include cp, ip, cur, obj, and other commands that enable a cursor. These commands will update the symbol keyhit to the value <Esc> when they trap an escape event.
eva evaluates an arithmetic expression and places the formatted result into the value field of the symbol. The parameter expression must be enclosed in parentheses, for example:
In this example, the symbol count is given a value that is equal to five times the current value of the symbol row. The capabilities of the eva command and the syntax of expressions are described explicitly in Appendix B, Symbol Reference. Note that there are no spaces allowed between the parentheses.
See also
def Define Symbol
get Get Symbol Value
cdf Condition Define
ex causes control of FELIX to change from interactive to macro execution mode. During execution of a macro, FELIX no longer accepts input from the user keyboard. Upon termination of macro execution, FELIX returns to the user and interactive control is returned to the keyboard (the > prompt appears on the screen and signifies the end of macro execution). Macros may also be executed with the file_name parameter.
Within a macro, the ex command causes another macro to be executed. All traces of the first macro executed are removed from memory. To call a second (or third) macro as a subroutine and return to the current macro, the macro call command (cal $macro_name) or execute and return command (exr macro) must be used within the parent macro. For a full discussion of macros, see Chapter 4, Macros.
Arguments may be passed to the macro. See "Passing arguments to macros" on page 30.
Symbol changed
macfil Current Macro File
See also
cal Macro Call
exm Execute Multiple Macros
exr Execute Macro and Return
go Macro Goto
exc causes the real and the imaginary parts of the work space to be exchanged. This command is most often used when you must merge the real component of a real T1 FID with the real component of an imaginary T1 FID (i.e., hyper-complex data acquisition. See States 1983).
Symbol dependence
datsiz Number of Data Points
datype Data Type
exm executes a macro while preserving the existing mscro memory and context. exm may be invoked from anywhere in FELIX -- the command line, the menu interface, or a macro. The executed macro is deleted after it completes the job.
Arguments may be passed to the macro. See "Passing arguments to macros" on page 30.
See also:
exr Execute a Macro and Return
ex Execute a Macro
exp generates an expanded display of the workspace using the current 1D plot limits (first, last).
Symbol dependence
first First Data Point
last Last Data Point
See also:
ful Full Plot
dr Draw Workspace
old Old Plot Limits
Execute a macro and then return to the current macro, continuing with the line immediately following this exr command. The called macro is deleted after it completes, and the current calling macro is not disturbed. Contrast this with ex and cal.
Arguments may be passed to the macro. See "Passing arguments to macros" on page 30.
See also:
ex Execute Macro
cal Call Macro
ret Macro Subroutine Return
fit invokes a line fitting subsystem of FELIX for optimizing peak parameters to yield a least squares fit to a spectrum. Peaks may be pre-picked using pic or created within fit. Single peaks may be added, removed, or manually edited.
Three independent optimization algorithms are provided within fit. These are simplex, quasi-Newton, and simulated annealing. You can select an algorithm and determine the set of peak parameters to be optimized. If you save the fitted peaks, the 1D peaks entity is updated with the new fitted values.
This command fits ND peaks in the temporary entities peak_entity and volume_entity using quasi-Newton minimization of the requested parameters (optimize_center= 1, optimize_widths = 1, and/or optimize_heights = 1).
Symbol dependence:
datsiz Number of Data Points
picent 1D Peaks Entity
See also
pic Pick Peaks
ssp Synthesize Spectrum
flf provides functions for baseline correction of the data in the work space, using the FaceLift algorithm published by Chylla, R. A. & Markley, J. L. (J. Mag. Reson. Series B 102, 148-154 (1993)).
flf baseline performs FaceLift baseline modeling on the data in the workspace. It identifies the baseline points and generates a model baseline. The generated baseline either overwrites the workspace (if buff_no is 0) or is stored in a buffer while the workspace remains unchanged (if buff_no is greater than 0).
flf correct performs FaceLift baseline correction on the data in the workspace. It is very similar to subcommanded flf bas, except that the baseline is directly subtracted from the original spectrum in the workspace.
flf smooth performs a (2 * filter_width + 1)-point binomial filtering on the data in the workspace. The smoothed data are stored in buffer buff_no.
See also:
abl Automatic baseline flattening
abq Automatic selection of baseline points
bas Baseline points manipulation
csp Cubic spline baseline correction
flt FLATT baseline flattening
smo Binomial smoothing
The fli command manipulates frequency lists. These lists provide a succinct method of storing chemical shift values that are believed to arise from a single residue. Chemical shift values may be added, deleted, filtered, or displayed from the frequency lists by using these commands. After examining a particular residue, the frequency lists associated with that residue may be written to a database frequency list entity for future use. Conversely, one can read chemical shift values into a frequency list from a database frequency list entity. FELIX provides eight frequency lists and allows storage of up to 64 chemical shift values in each list.
The clear subcommand removes all values from the specified frequency list.
The add subcommand appends chemical shift values to the frequency list. Any number of chemical shift values may be specified on the command line although each frequency list stores a maximum of 64 values.
The list subcommand lists (on the screen) the chemical shift values stored in the specified frequency list.
The delete subcommand removes chemical shift values that are greater or equal to lo_freq, and less than or equal to hi_freq, from the specified frequency list.
The union subcommand combines frequency lists one and two into frequency list three. Unique chemical shift values are transferred to frequency list three from either of the source lists. In the case of two equal frequencies in each source list, union adds just one instance of the chemical shift value to frequency list three.
The draw and object subcommands store graphical representations of frequency lists one and two in the specified object. The chemical shift values in frequency list one appear as vertical lines of the requested color and the values in list two appear as horizontal lines of the requested color. The obj# parameter determines the destination for the drawn frequency lists. When obj# is positive, the frequency lines are placed into a graphical object for later display. When obj# is zero, the frequency lines are drawn immediately on the current 1D or 2D plot. If the D1color or D2color is -1 then each frequency in the list will have a different color.
The tile subcommand uses the chemical shift values in frequency lists one and two, as well as the tile_width factor, to create a tile entity with the name tile_entity.
See also
cp Contour Plot
ip Intensity Plot
til Tile Plot
The read subcommand copies the chemical shift values in the database frequency list entity freq_entity to the specified frequency list.
The write subcommand copies the chemical shift values in the specified frequency list to the database frequency entity freq_entity.
The move subcommand copies the chemical shift values in list1 to list2.
The equiv subcommand removes nearly equal chemical shift values from a specified frequency list and replaces the two values with their average. Two chemical shift values are considered to be nearly equivalent when the difference between their values is less than resolution.
The xpeaks subcommand creates a frequency list from a list or entity of cross peaks. A frequency is made at each center along the given dimension, then all frequencies closer than resolution are combined.
The peak subcommand creates a frequency list from a list or entity of 1D peaks. A frequency is made at each center, then all frequencies closer than resolution are combined.
The an subcommand appends chemical shift value and names to the frequency list one by one. Each frequency list stores a maximum of 64 values and names.
The rc subcommand copies the chemical shift values and names in the assign database frequency clipboard entity clipboard_entity to the specified frequency list.
The rn subcommand copies the chemical shift values and names in the assign database pattern entity pattern_entity to the specified frequency list. You have to specify which pattern's (pattern_#) chemical shifts to copy and whether to use the generic shifts (spectrum_id = 0) or spectrum specific shifts (in that case the spectrum_id should reflect that experiment's number).
The rp subcommand copies the chemical shift values and names in the assign database protopattern entity protopattern_entity to the specified frequency list. You have to specify which protopattern to copy (proto_#).
The collect subcommand collects frequencies from the assign database pattern entity into the specified frequency list. All frequencies will be copied which generic (spectrum_id = 0) or spectrum specific shifts (spectrum_id =n) are within delta ppm from the specified centrum position.
The sort subcommand will sort the content of the specified frequency list in descending (order=0) or ascending order (order=1) by the chemical shifts.
flp performs a low-point fold on the data in the workspace by saving the lower value of the two symmetrical points (for data that has a size of 1024 points, point 1 is compared with point 1024; point 2 with point 1023; point 3 with point 1022; etc.). The command flp is similar to the fold data command (fol) and can be used if you know that the workspace contains symmetric data. By performing a low-point fold on the workspace, the size is decreased by a factor of two. This command is convenient for non-diagonal symmetrization of multidimensional spectra.
Symbol dependence
datsiz Number of Data Points
datype Data Type
Symbol changed
datsiz Number of Data Points
See also
fol Fold Workspace in Half
unf Unfold Data
This command performs FLATT baseline correction on the data in the work space. flt automatically identifies the segments of data in the work space that constitute the baseline. The command fits a Fourier synthesized curve to the baseline points using a linear-least-squares fit, based on a singular value decomposition, and subtracts the synthesized curve from the data in the work space. The FLATT baseline correction was introduced by Güntert and Wüthrich in 1992 (please see the FELIX User Guide for the full reference).
flt uses the baseline_width, chimin, and tau parameters to find baseline segments in the spectrum. The baseline_width parameter determines the width of a sliding window that flt uses to identify baseline segments. flt moves the window point-by-point along the length of the spectrum, fitting the spectral data points within the window to a straight line, calculating the chi square value of the fit, and storing the chi-square value in a vector. Next, a narrower window of width 2/3basline_width is moved point-by-point along the vector of chi-square values. If the smallest chi-square value within the window is less than the product of the parameters chimin and tau, flt considers the point in the center of the window to be a baseline point. The number_of _points parameter determines the number of terms used in the Fourier synthesis.
Symbol dependence
chi Minimum Chi-square Value
See also
chi Calculate Minimum Chi-square Value
flf FaceLift baseline correction
fol performs a linear symmetrization of the 1D workspace by co-adding the first and last points together; second and next-to-last points; etc., until a "new" symmetrized, 1D spectrum is created. By performing a co-addition fold on the workspace, the size of it is decreased by a factor of two. This command is convenient for non-diagonal symmetrizations of multidimensional spectra.
Symbol dependence
datsiz Number of Data Points
datype Data Type
Symbol changed
datsiz Number of Data Points
See also:
flp Low-point Fold of Workspace
unf Unfold Data
for is the FELIX macro loop operator, which acts in a manner very similar to the BASIC computer language FOR command. The for command may only be used in macros. Within a macro, the for command allows all of the commands between itself and the macro command nex to be executed, incrementing the value of symbol by step each cycle through the loop. The for command is mainly used to loop through rows and columns of matrices while performing multidimensional transforms. Like the BASIC FOR command, FELIX for loops may be nested within each other as long as each for loop has a nex command defining the end of the loop.
With this command, you can pop the FELIX window on top of any window residing in the same position on the screen. This command is useful if you use FELIX with Insight II, and wish to bring FELIX into the foreground from within a macro.
With this command you can push the FELIX window to the background, i.e., behind any window residing in the same position on the screen. This is useful if you are using FELIX with Insight II, and want to push FELIX into the background from within a macro.
fra allows you to define a number of graphics frames in the FELIX window and to direct graphics to these frames. Each frame maintains its own complete graphics context, which includes the 1D workspaces, all user and reserved symbols, and matrix. Only one frame is current at a time. For example, displaying the workspace in the current frame modifies only the graphics context for the current frame. All other frames will maintain their original graphics context.
The frame operators and their functions are as follows:
fra open opens a new frame. Origins and sizes are given in pixels. A newly opened frame becomes the current frame and inherits the graphics context of the previously current frame. Specifying the x_origin as -1 opens a default size and position frame.
fra zero closes all frames and re-initializes the frame manager.
fra front pops any frame to the front of all other frames. The specified frame also becomes the current frame. Specifying a frame# of -1 allows the desired frame to be identified by clicking anywhere within the frame.
fra close closes the current frame. The graphics context of the closed frame is discarded. The next-most-current frame then becomes the current frame.
fra move moves the current frame to a new position with its origin at the position specified by the pixel parameters x_origin and y_origin. Specifying an x_origin of -1 allows you to move the frame using the mouse.
fra resize allows the current frame to be re-sized and re-positioned anywhere within the FELIX window. The origin and sizes are in pixel units. Specifying the x_origin as -1 allows manual re-sizing of the current frame using the mouse.
fra verify allows you to verify or inquire about the existence of a frame by number. If the specified frame exists, the value 1 is stored in symbol. A value of 0 is stored in symbol if the frame does not exist.
fra header allows you to label the frame header with a text string. The text should be enclosed within single quotes if you wish to preserve upper case characters and blanks.
fra who allows you to inquire which frame is current. The frame number of the current frame is stored into symbol. A zero will be stored in symbol if no frames exist.
fra 3D_reset resets the 3D viewing parameters. By default, the 3D display interface does not reset the rotation, translation, scaling, and clipping parameters. This allows you to maintain the exact view of a 3D object between plots. This frame operator resets all the 3D display parameters to initial values, just like the set button in the 3D display interface.
fra xpand expands the current frame to cover all other frames. This enhances the pixel resolution to show more detail. The current plot is automatically redrawn.
fra unexpand restores an expanded frame to its previous size and location. The current plot is automatically redrawn.
fra j iconifies the current frame. The current plot is automatically redrawn.
fra k restores an iconified frame to its previous size and location. The current plot is automatically redrawn.
All the above fra operations act upon the single current frame. Recall that each frame has its own complete graphics context including graphics, symbol values and data. For example, when you change to a different current frame, the 1D workspace is overwritten with the new frame's copy of the workspace contents.
The following fra operators facilitate the transfer and sharing of context between pairs of frames:
fra export exports the entire context of the current frame to another frame. The current frame does not change and its context is not affected.
fra import imports the entire context from another frame into the current frame. The graphics context, symbols and data are changed in the current frame, which becomes an exact copy of the specified frame's context.
fra symbol is used to pass a single symbol value between the current frame and another frame. This operation is frequently used when working with correlated displays of corresponding regions of different spectra.
The mode parameter allows transfer of context symbols either into or out of the current frame. When mode is zero, the value of symbol_name is transferred from the other frame frame# to the symbols local_symbol in the current frame. When mode is one, the value of symbol_name is transferred to the symbol of the same name in the other non-current frame frame#.
The following fra operators facilitate the connection of frames-using this command you can assure that navigating in one frame will update the plot limits in other frames:
fra q cleans up the frame connections. It is necessary to call this if you need to start a new frame connection setup.
fra add adds a frame to the frame connection list, subsequently the fra l(ink) command should be called to set up the dimension connections.
Link dimension_a of frame_n to dimension_b of frame_m after both frame_n and frame_m were defined as linked by the fra a(dd) command. If dimension_a or dimension_b are less than or equal to zero, the connection along that dimension gets broken. If both are less than or equal to zero, the link gets cleaned up.
Define a jump from dimension_a of frame_n to dimension_b of frame_m after both frame_n and frame_m were defined to be linked by the fra a(dd) command.
If later the fra y command without parameters is called from frame frame_n then you can click a position in frame_n and that will define a new plane position in frame_m along dimension_b.
Execute the jump in the current frame if previously the current frame was put on the connection list via fra a command and the jump was defined using the fra y command.
Temporarily disables frame connection
Restores frame connection if it was defined before.
ft performs a complex fast Fourier transform on the contents of work. The ft command runs faster if the size of the data in the workspace is a power of two, but it will transform any size of data.
If the symbol gibbs is set to 1, the first and last point of the workspace are divided by two before transformation to properly weight the time period these samples represent. If gibbs is set to 0, the division is not performed.
Symbol dependence
datsiz Number of Data Points
gibbs Gibbs Filter Switch
See also
dft Oversampled Bruker Fourier Transform
rft Real Fourier Transform
bft Bruker-Fourier Transform
ift Inverse Fourier Transform
hft Hilbert Transform
ful draws the entire 1D spectrum in the current frame. ful is the opposite of the exp command.
Symbol changed
First First Data Point
last Last Data Point
See also
exp Expand 1D Plots
old Old Plot Limits
fxp provides operators for various types of cross peak filtering. fxp is used after picking peaks to remove unwanted peaks and eliminate redundant peaks.
Symbol dependence
hafwid Cross Peak Half Width Factor
This operation removes all diagonal peaks from a square matrix or from a non-square matrix if the units parameter is set to ppm and on of the type parameters is set. If the peak center along each dimension is within tolerance points of centers for that peak in all other dimensions, the cross peak is considered to be on the diagonal and will be deleted.
This operation combines multiplet peaks into single peaks. If any two peak centers are within tolerance points of each other along all dimensions, the two peaks are combined into one larger peak with a footprint that covers all the multiplet footprints.
This operation removes asymmetric peaks from a 2D square matrix. If the optional units and type parameter is specified the matrix can be a non-symmetric 2D, 3D or 4D. For every peak in the peaks entity, a search occurs for a peak located within tolerance points of the symmetrical position. If no peaks are found within this distance, that cross peak has no symmetric partner and is deleted from the peaks entity.
This operation removes peaks from the database if their width is less than the minimum width (min_width) parameter or greater than the maximum width (max_width) parameter.
get is used to prompt for data from within a macro. The command get issues the specified prompt (entered as the prompt_string) when executed in the macro, then waits for you to enter a value for the defined symbol_name. The value of the specified symbol is set to the data value entered. Enclose the prompt_string in single quotes if you wish to preserve uppercase letters and spaces.
See also
def Define a Symbol
lis List Symbols and Values
gf allows you to generate an FID containing as many lines as you wish. The amplitude is in arbitrary units. The frequency is in Hz, and the tau is the time constant of the decay in seconds, or (1/linewidth in Hz). If you let the program prompt you for input, you can continue adding lines until you are done, then terminate gf with a zero amplitude.
Symbol dependence
datsiz Number of Data Points
datype Data Type
gif branches to a label depending on the numeric value of expression. If expression is negative, zero or positive, gif branches to label1, label2, or label3 respectively. This command is valid only in macros.
gm acts in the same manner as the gm command found on Bruker spectrometers. The command gm is generally used to enhance resolution at the expense of sensitivity. If the broadening and coefficient parameters are not entered, the reserved symbols for line broadening (lbroad) and Gaussian parameter (gbroad) are used. Typically, a negative broadening parameter is used with the coefficient parameter of 0.2 to give a Gaussian component to the line shape.
Symbol dependence:
swidth Spectral Width in Hz
datsiz Data Size
datype Data Type
gmh multiplies data in the work space by a Gaussian window. Gaussian apodization, rather than Lorentzian multiplication (em), is useful in processing data whose inherent line shapes are Gaussian as is the case for most solid state NMR spectra. This command does not introduce apodization errors that will adversely affect the data in later quantization, fitting, or deconvolution, because it does not change the line shape from Gaussian to a Gaussian-Lorentzian mixture (Gladden 1986). The gmh command may also be used in constructing customized apodization function for two-dimensional processing.
go is used within macros to perform an unconditional branch to the specified label.
scaling of text -- fixed (0), according to Y size of plot (1), according to X size of plot (2), according to both sizes (3 |
|
centering -- left justify (0), center point (1), right justify (2) |
|
gre draws text with its origin at (x0, y0) (optionally z0 and a0 if strip plot of a 3D or 4D matrix). The coordinates are interpreted based on the symbol annunt. All 24 Greek characters can be drawn, in both upper and lower case. The text is translated from the Roman to Greek alphabets as shown below:
Symbol dependence
anncol Annotation Color
annunt Annotation Units
annang Annotation Angle
annsiz Annotation Text Size
slant Annotation Text Slant
thick Text Thickness
See also
tex Text Annotation
ann Annotate Plot
gto branches to the nth label based on the value of the expression in the range 0:n. If the expression value is less than zero or greater than n, no branch will occur. This command is valid only in macros.
gsp generates an FID from the input parameters. The gsp command prompts you for the parameters of a set of lines and then generates a spectrum with these lines. Parameters include intensity, frequency, Gaussian, and Lorentzian line widths. If both Gaussian and Lorentzian line widths are specified, a Voigt line shape is computed. gsp adds the lines to the data in the work space, so the work space should be set to zero before you use this command. gsp generates only real data, therefore if you need a complex spectrum, a Hilbert transform (hft) must be performed on the FID.
gv gets the value of the specified data point and assigns the value to the defined symbol(s). If the point number is outside the range of 1 to frsize (maximum frame size), no action is taken. The symbol for the imaginary part is optional, and will be ignored in the case of real data.
Symbol dependence
datype Data Type
hav halves the size of the workspace by averaging successive pairs of points. The hav command works in a manner opposite the double data size command (dbl)
Symbol dependence
datsiz Number of Data Points
datype Data Type
Symbol changed
datsiz Number of Data Points
hcp generates a hard copy plot similar to the current plot on the screen. The plot format is determined by the value of the symbol hardmo; when hardmo is set to 21, the plot format is PostScript, and when it is set to 31, the plot format is HPGL. The output is sent to the device specified by the harddv symbol, which can be the name of a file, the name of a computer port, or a UNIX print command. For the command hcp to work properly, there must be a current plot in the current frame. Hard copy plots may also be generated from within the menus.
The width and height of the paper used to make the plot may be specified by defining the symbols papwid and paphgt, respectively, in inches. Under certain conditions, FELIX can use this information about the paper size. These conditions are described below.
When making PostScript plots, FELIX defines the EPS bounding box to enclose the outline of the page. Furthermore, when making PostScript plots in the landscape orientation, FELIX resets the plot origin based on the page height. When making HPGL plots on plotters that assume the axis origin is in the center of the page, FELIX uses the page size to shift the axis origin down one-half page height and to the left one-half page width.
The position and size of the plot on the page are specified by the symbols hardx0, hardy0, hardxs, and hardys. The first two symbols define the position of the lower left corner of the plot, in inches, relative to the axis origin of the plotter (after adjustments to the axis origin that result from setting the symbols paphgt, papwid, pltorg, and orient). The symbols hardxs and hardys determine the dimensions, in inches, of the area in which FELIX may make the plot, exclusive of the axis labels. The actual dimensions of intensity, contour, and stack plots depend on the number of points in each dimension and the scale factors for each dimension (as set by the sca command), but the corners of the plot will always fit within the area defined by hardxs and hardys. Note that the axis origin of the printer/plotter may not lie exactly at the corner of the page so you may need to adjust the hardx0 and hardy0 to obtain the result you want.
FELIX produces the plot in either landscape or portrait orientation, depending on the value of the orient symbol. For plots in landscape orientation, set orient to zero, and for portrait, set orient to one.
FELIX generates text characters on plots either by generating series of vector draws in order to form the required text or by using the fonts built into the plotter or the printer. You select the method to be used by setting the fontsw symbol to zero for the vector stroke generator or to one for the internal fonts of the plot device.
The graysc symbol modifies the color indices to produce a grayscale with PostScript devices. When graysc is set to zero, the color indices are used unmodified. Thus, with non-color PostScript printers, contours or intensities of increasing value will be rendered in shades of gray that correspond to the intensity of the color identified by the increasing color indices, that is, not in uniformly varying steps of gray. However, setting the graysc symbol to 1, causes the color indices to be interpreted as uniformly varying steps of gray. This symbol has an effect on PostScript output only.
Some plotters that understand HPGL set the default position of the axis origin near the lower left corner of the page and others set the origin near the center of the page. In the latter case, setting the pltorg symbol to 1 causes FELIX to reposition the axis origin from the page center to the lower left corner. FELIX determines the required shift by dividing the values of the symbols papwid and paphgt by two. If the plotter positions the axis origin at the lower left corner by default, then set pltorg to zero so that FELIX leaves the origin position undisturbed.
Some HPGL pen plotters may not communicate coherently with the computer to which they are connected. The communication problem is manifested by what amounts to scribbles on the paper after a small portion of the plot is drawn correctly. The problem results from inadequate handshaking signals exchanged between the plotter and the computer. The handshaking is performed either by software (XON/XOFF) or by hardware (using the RS-232C RTS, CTS, DTR, and CDC lines). In brief, the computer transmits instructions to the plotter far faster than the plotter can execute the instructions. The plotter has a small buffer of memory to store incoming instructions, but this memory is quickly filled. Before the memory reaches its limit, the plotter sends a signal (XOFF for software handshaking or DTR for hardwire handshaking) to the computer requesting that the computer stop sending plotter instructions until instructed to resume. If the computer responds promptly, there is no problem. Otherwise instructions are garbled as they flood into the full buffer, resulting in scribbles on the plot.
The problem may be solved either by using hardwire handshaking (if the computer supports the RS-232C RTS, CTS, DTR, and CDC lines and the cable from the computer to the plotter is correctly wired) or by using software handshaking and instructing the plotter to send its XOFF command to the computer well before the buffer is full. FELIX provides four options for setting the plotter communications. The options are selected by the hndshk symbol. When hndshk is set to 0, the plotter is instructed to use software handshaking and to send the XOFF signal when 181 bytes of memory remain in the buffer. This is the value used in earlier versions of FELIX. Setting hndshk to 1 instructs the plotter to send the XOFF signal when 1023 bytes of memory remain in the buffer; in fact, this means that the plotter is instructed to send the XOFF after one byte enters the buffer. This may solve most incidents of buffer overflow but it may slow the plotting rate, especially if the serial port is set to a low BAUD rate. If you want to tailor the plotter handshaking yourself, you may set the hndshk symbol to 3 and create a file named pref.31 (which contains the appropriate initialization instructions for the plotter) in the directory in which you run FELIX. In this case, when you issue the hcp command, FELIX appends the contents of the pref.31 file to the beginning of the plot file. Finally, you may interconnect the computer and plotter with a cable that transmits the hardwire handshaking signals properly and set hndshk to the value 2 to enable hardwire handshaking.
Symbol dependence:
hardmo Hard Copy Mode
harddv Hard Copy Destination
disply Current Plot Type
papwid Paper Width
paphgt Paper Height
hardx0 X Origin
hardy0 Y Origin
hardxs X Size
hardys Y Size
orient Plot Orientation
fontsw Font Switch
graysc Gray Scale (PostScript Only)
pltorg Axis Origin (HPGL Only)
hndshk Handshake Parameters (HPGL Only)
See also:
dr Draw Workspace and Stack
ip Intensity Plot
cp Contour Plot
sp Stack Plot
sca Scale Factor for Dimension
hft performs a Hilbert transform on real data in the workspace by converting a real vector into a complex vector. It is important that the number of points in the workspace be power of two. The Hilbert transform generates the imaginary (dispersive) part of the spectrum from the real vector and is useful for phase correcting frequency-domain data that has no imaginary part. Once hft generates the imaginary data, you may use the inverse FFT (ift) to transform the data into time-domain data. Many useful processing tricks can be performed only in the time domain, thus the Hilbert transform is useful for converting real data to time-domain form.
If the mode parameter is set to 1 then a different and more precise algorithm is used (Ernst 1969, Zolnai 1990, Rance private communication).
Symbol dependence
datsiz number of data points
See also
ft Fast Fourier Transform
bft Bruker-Fourier Transform
ift Inverse Fourier Transform
rft Real Fourier Transform
The idf command tests to see if a symbol is defined. If test_symbol is defined, then ans_symbol is set to 1. Otherwise, the value is 0.
See also
cdf Conditional Define
def Define a Symbol
pur Purge Symbols
if compares expression1 and expression2 according to the relational operator, defined by operator. Two classes of relational operators are provided; one compares expressions as a string of characters, while the other first converts the expressions to real numbers. If the condition is true, control transfers to the specified macro label; if it is false, no branch occurs. There are 12 legal relational operators:
1. Sub-string Specification: For string comparisons, there is a syntax for specifying a substring on which to base the comparison. To specify a substring, append (first_char:last_char) to the end of expression, with no intervening spaces. This means to consider only the characters beginning with first_char and ending with last_char in the comparison.
2. Compound Conditionals: All forms of the if command also support compound conditionals. You can combine two or more conditionals in one if command by separating them with the keywords and or or.
if exp op exp then
.
. {block of commands}
.
The block if evaluates the condition as described above. If the condition is true, all commands in the block up to the eif are executed. If the condition is false, execution skips to the command following the eif.
if exp op exp then
.
. {true block of commands}
.
els
.
. {false block of commands}
.
The if/then/els evaluates the condition as described above. If the condition is true, the block of statements between then and els is executed, then execution skips to the command following the eif. If the condition is false, the block of commands between the els and eif commands is executed.
Due to block ifs and compound conditionals, the reserved keywords then, and, and or may not be used as labels in an if command.
ift performs an inverse Fourier transform; it transforms a complex frequency-domain spectrum into a complex time-domain FID.
Symbol dependence
datsiz Number of Data Points
gibbs Gibbs Filter Switch
datype Data Type
See also
dft Oversampled Bruker Fourier Transform
ft Fourier Transform
rft Real Fourier Transform
bft Bruker-Fourier Transform
inq is used to determine if a specified file already exists or not. inq sets symbol to zero if the file does not exist and to one if the file does exist. When ext is a known file extension (dat, mat, mac, dba, ann, mnu), the corresponding prefix and extension will be used. When the extension is null, no prefix or extension will be used.
Symbol changed:
The symbol specified as a parameter is set to zero or one.
The ins initialize command initializes the FELIX server.
The ins connect command connects FELIX to Insight II.
The ins check command checks to see if the RPC connection is currently up
ins command passes the command string to Insight II, substituting the atom specification from the NMR spec into an Insight II spec.
ins command2 passes the string to Insight II as is, without converting the data format.
The ins getdir command gets the current directory from Insight II.
The ins command has operators to facilitate communication between FELIX and Insight II. This allows the two programs to interact whenever they are being run simultaneously.
All the ins commands set the symbol instat to show the resulting status of that ins call. A status of zero (0) denotes success, while a non-zero status indicates an error.
init initialize the FELIX server
connect connect FELIX to Insight II
check check if RPC connection is currently up
command send a no reply wanted command to Insight II
getdir get the current directory from Insight II
int generates the integral of the data in the workspace and pushes it onto the display stack. For optimal results using the int command, a level baseline is necessary.
Symbol changed
stack Stack Depth
inv replaces the data in the workspace vector by its inverse. The inv command takes the reciprocal of each point in the workspace (replaces work by 1/work) and stores the new value back in the workspace. If there are any zero points in the workspace, they are skipped to avoid a divide by zero error. inv can be used to create novel and useful window functions for apodization.
ip draws an intensity plot of the current plot region on the graphics device. The default rendering mode erases the screen before each display; this action may be defeated by setting the reserved symbol erase to 1.Video buffering may be enabled by setting the reserved symbol animat to 1. The behavior of the command ip is affected by a number of other reserved symbols.
Symbol dependence
animat Specify Video-Buffering
clmode Selects Linear or Geometric Contour Spacing
conmod Contour Level Modifier
cycle Sets Color Cycle
drwbox Draw Box Around Plot
level First Contour Level
nlevel Number of Contour Levels
posneg Enables Plotting of Negative Contour Levels
projct Select Dimensionality of Display
pennum First Color
rowinc Point Skipping Factor For 3D Displays
Symbol changed
disply Current Display Type
See also
cp Contour Plot
np Null Plot
sp Stack Plot
pla Fast Re-plot of 3D Object
rmx Reference Matrix (Sets Axis Type)
item of selected peak (-1 enables crosshair to select) (-2 enables crosshair to select E-COSY peak) |
|
symbol to receive sigma of J coupling value along dimension N |
jcp calculates J coupling constants by fitting multiplet footprints. This command destroys the contents of the work space and yields coupling constants for both dimensions along with standard error. Be aware that apodization functions can alter the observed line shapes of antiphase multiplets and affect the values calculated by jcp. This should be considered a somewhat crude measurement.
If item is set to -2 then the program allows you to drag two subpeaks of an E-COSY multiplet, and the optimized J coupling values are returned to jNval variables.
The optimization method used in determining the coupling constant can be either quasi-Newton, simplex, or simulated annealing depending on the optmth symbol. The default is quasi-Newton minimization.
Symbol dependence:
optmth optimization method for DQF-COSY or E-COSY J coupling extraction: Quasi-Newton (0), simplex (1) or simulated annealing (2).
kw is a window function described in Hamming's book Digital Filters. This window is useful for apodizing truncated data.
ld lists the values of the data in the work space. If no parameters are entered, data values for all of the points in the work space are listed.
ldb loads the contents of the specified buffer into the work space.
Symbol dependence
datsiz Number of Data Points
datype Data Type
nframe Number of Buffers
See also
adb Add Workspace to Buffer
stb Store Work Space to Buffer
sp Stack Plot
lim is used to select regions of multidimensional matrices for display on graphics devices. Matrix subsets are defined by specifying the first and last data points defining the boundaries of the subset for each matrix dimension using the lim command. (For example, by typing lim 1 1 50, lim 2 1 50, lim 3 1 50, you would define the limits of a 3D subset, in this case a cube.) Projections (or slices) of a matrix may also be defined by setting the first and last points of one of the limits to the same number for one or more dimensions, thus decreasing the dimensionality of the data. (For example, lim 1 25 25, lim 2 1 50, lim 3 1 50 would define a 2D slice of a 3D matrix taken through point 25, along dimension 1). To list the current matrix limits, the lim 0 command may be entered. Other forms of the lim command include:
Sets limits with the rubber band box cursor.
Resets limits to their previous designation; like old for 1D.
Sets full ND limits, like ful for 1D.
Symbol changed
lolimn Low Limit For Dimension N
hilimn High Limit For Dimension N
See also
bld Build Matrix
mat Open Matrix
cp Contour Plot
ip Intensity Plot
ord Matrix Dimension Order
lin draws a line (solid or dashed depending on the symbol annlst) from (x0, y0) to (x1, y1). The optional coordinates are useful if the matrix is a 3D or 4D and the current plot is a strip plot. The line should be drawn starting in one strip and ending in another strip, where the strips are taken from different slices of the ND matrix. The color of the line is determined by the symbol anncol. The units of all coordinates are interpreted based on the symbol annunt and may be specified in a variety of units.
Symbol dependence
anncol Annotation Color
annlst Annotation Line Style
annunt Annotation Units
See also
arr Arrow Annotation
rec Rectangle Annotation
ann Annotate Plot
lis displays current symbols and their values. The optional specifier may contain a * wildcard to list only specified symbols.
lm lists the current or specified macro.
loa loads the specified vector from a matrix into the work space. For example, loa 0 1 would load the vector along D1 that passes through point 1 of D2; and loa 1 0 would load the vector along D2 that passes through point 1 of D1. loa must be given exactly one parameter that is zero. You can think of the zero as specifying the dimension along which the vector is loaded, and the other parameters locating the vector position in all other dimensions.
Symbol changed
dnvect Vector Coordinates Along Dimension N
datsiz Number of Data Points
datype Data Type
sfreq Observe Frequency
swidth Spectral Width
refsh Reference Shift
refpt Reference Point
first First Point
last Last Point
disply Current Display
See also
sto Store Vector to Matrix
lwb Load Workspace From Bundle
log replaces each data point in the workspace with its natural (base e) logarithm. The log command may be used to compute some novel windows for apodization. If a data point in the workspace is less than or equal to zero, it is set to zero to avoid a mathematical error.
Symbol dependence
datsiz Number of Data Points
See also
aln Antilogarithm (Exponential) of Workspace
lmd loads the specified vector from a theoretical matrix into the work space similarly to the loa command. Therefore you must first issue the data modeling command (md) to display the theoretical matrix. The loaded vector contains data from the peak and volume entities. For example, lmd 0 1 would load the vector along D1 that passes through point 1 of D2; and lmd 1 0 would load the vector along D2 that passes through point 1 of D1. lmd must be given exactly one parameter that is zero. You can think of the zero as specifying the dimension along which the vector is loaded, and the other parameters locating the vector position in all other dimensions.
Symbol changed
dnvect Vector Coordinates Along Dimension N
datsiz Number of Data Points
datype Data Type
sfreq Observe Frequency
swidth Spectral Width
refsh Reference Shift
refpt Reference Point
first First Point
last Last Point
disply Current Display
lpf uses linear prediction to estimate the values of incorrectly acquired first points using subsequent data points. lpf determines coefficients-LP coefficients based on data points numbered (1 + first) through points. New data values are generated backwards from point first to point one.
Suggestions for choosing the parameters include setting points to the number of data points in the FID and setting coefficients to one-quarter to one-third the value of points. However, if there are more than several hundred data points in the FID, lpf may require more than tens of seconds to perform its work. If this occurs, choose smaller values for these two parameters by selecting a value for coefficients that is greater than the number of signals in the FID and setting points to three or four times the value of coefficients.
The peaks parameter is left in for compatibility with older macros, but its value is not used in the calculation.
Symbol dependence:
datsiz Data Size
datype Data Type
See also:
lpl Linear Predict Last Points
lpl uses linear prediction to extrapolate additional points from existing time-domain data. This command can be used as an alternative to zero-filling or apodization when dealing with truncated data. lpl determines coefficients-LP coefficients-based on data points 1 through points. New data values are generated for points first through last. If last is greater than the number of data points, the datsiz symbol is set to last. The root reflection flag enables reflection of roots that fall outside the unit circle, which ensures that the linear prediction coefficients represent decaying signals. Set reflect to 1 to enable root reflection, and to 0 to disable it.
Suggestions for choosing the parameters include setting points to the number of data points in the FID and setting coefficients to one-quarter or on-third the value of points; however, if there are more than several hundred data points in the FID, lpl may required more than tens of seconds to perform its work. If this occurs, choose smaller values for these two parameters by selecting a value for coefficients that is greater than the number of signals in the FID and setting points to three or four times the value of coefficients.
The peaks parameter is left in for compatibility with older macros, but its value is not used in the calculation.
Symbol dependence
datsiz Data Size
datype Data Type
See also
lpf Linear Predict First Points
lps subtracts the largest signal(s) from the time domain data, which accomplishes solvent signal suppression. The algorithm uses singular value decomposition to determine the singular values of the data matrix. These singular values and the signal amplitudes are correlated such that the highest amplitude signals have the largest singular values. The command uses this fact and additional information from the singular value decomposition (SVD) to generate a set of data points that are nearly identical to the highest amplitude signal(s) in the data set, and which is subsequently subtracted from the data. points sets the number of points used to create the data matrix for the singular value decomposition. The number of peaks you wish to subtract from the signal is set with peaks. When transforming data "blindly", as in macros, it may be useful to prevent signal subtraction when the peaks signal is not significantly larger than the next largest signal. The threshold parameter accomplishes this by referring to the ratio between the peaks singular value and the (peaks + 1) singular value. If the ratio falls below threshold, the subtraction will not occur.
See also:
cnv Time Domain Convolution
lpx uses linear prediction to extrapolate additional points from existing time-domain data. This command can be used as an alternative to zero-filling or apodization when dealing with truncated data. lpx determines coefficients -- LP coefficients -- based on data points use_first through use_last. New data values are generated for points predict_first through predict_last. If predict_last is greater than the number of data points, the datsiz symbol is set to predict_last. The root reflection flag enables reflection of roots that fall outside the unit circle, which ensures that the linear prediction coefficients represent decaying signals. Set reflect to 1 to enable root reflection, and to 0 to disable it.
The method can be either forward prediction (method=0) or backward (method=1). You can use forward-backward (Zhu and Bax 1992) prediction, which has been proven to be superior to the forward method, but is slower (method=2). If the FID does not decay, then you can also carry out mirror-image linear prediction (Zhu and Bax 1990) (method=3). In this latter case you have to set the mode parameter to reflect whether your data was collected with half dwell time shifted (0) or not (1).
Suggestions for choosing the parameters include setting use_first and use_last to include as many good points as possible from the FID, and setting coefficients to one-third or one-fourth the value of points; however, if there are more than several hundred data points in the FID, lpx may require more than tens of seconds to perform its work. If this occurs, choose smaller values for these two parameters by selecting a value for coefficients that is greater than the number of signals in the FID.
Symbol dependence
datsiz Data Size
datype Data Type
See also
lpl Linear Predict Last Points
lpf Linear Predict First Points
The lrl commands finds local minimum, maximum or extremum in the current spectrum.
lrl max finds the maximum intensity position within the defined box limits and stores the position into the symbol_pos1, symbol_posn; the intensity at that place is stored in symbol_int.
If (lopt1) is set to -1 it finds the maximum intensity position defined by the consecutive rubber box cursor:
If (lopt1) is set to 0 it finds the maximum intensity position within the current plot limits:
lrl min finds the minimum intensity position within the defined box limits and stores the position into the symbol_pos1, symbol_posn; the intensity at that place is stored in symbol_int.
If the first parameter (lopt1) is set to -1 then it finds the minimum intensity position defined by the consecutive rubber box cursor:
If (lopt1) is set to 0 then it finds the minimum intensity position within the current plot limits:
lrl ext finds the extremum intensity position within the defined box limits and stores the position into symbol_pos1, symbol_posn; the intensity at that place is stored in symbol_int.
If (lopt1) is set to -1 it finds the local extremum intensity position defined by the consecutive rubber box cursor:
lrl pma finds the maximum intensity position within the defined box limits (in ppm) and stores the position in ppm into symbol_pos1, symbol_posn; the intensity at that place is stored in symbol_int.
lrl pmi finds the minimum intensity position within the defined box limits (in ppm) and stores the position in ppm into symbol_pos1, symbol_posn; the intensity at that place is stored in symbol_int.
lrl pex finds the extremum intensity position within the defined box limits in ppm and stores the position in ppm into symbol_pos1, symbol_posn; the intensity at that place is stored in symbol_int.
lvo loads the volume time course for a single cross peak at all non-zero mixing times into the work space. This generates a set of x, y pairs in which x is time and y is volume. Use dr to display the volume time course, and xyp fit to fit the time course to a selected function. Peaks must have been picked and volumes measured before meaningful time courses may be loaded.
The optional start parameter can insert a zero volume at zero time (default action if no parameter specified or start=0) or not (start=1).
Symbol changed
datsiz Number of Data Points
datype Data Type
See also
mgv Matrix Get Value
gv Get Value
vol Measure Volumes
xyp X, Y Pair Manipulation
pic Peak Pick and Label
lwb is used to load the next bundle vector into the workspace. The vector may then be processed and returned to the bundle using swb.
Symbol changed
datsiz Number of Data Points
datype Data Type
sfreq Observe Frequency
swidth Spectral Width
refsh Reference Shift
refpt Reference Point
See also
bun Bundle Mode
loa Load Vector
swb Store Work to Bundle
mat opens an existing matrix; previously built with the build matrix command (bld). An open matrix may be accessed one vector at a time using the load vector from matrix command (loa). A new matrix may be filled with data using the sto command.
The storage parameter allows you to control whether the matrix resides on disk (default) or is read entirely into memory. If your workstation has enough RAM, storing the matrix in memory speeds up most processing and plotting functions. If you attempt to store the matrix to memory and there is not enough space available, the matrix will simply stay on the disk and no error will be flagged.
Symbol dependence
matpfx Matrix Prefix
Symbol changed
dimen Dimensionality of Matrix
d1size D1 Size
d2size D2 Size
d3size D3 Size
d4size D4 Size
b1size D1 Brick Size
b2size D2 Brick Size
b3size D3 Brick Size
b4size D4 Brick Size
matfil Matrix File
md allows you to display any linear combination of real and modeled N-dimensional data. To use md, first pick peaks using pic and measure volumes using vol. These two steps define the model cross peak shifts, line widths, and intensities. Next, use the md command to enable display of model data. The effects of md stay in effect until disabled by setting model to zero. Modeled data can be displayed using cp, ip, and sp.
mf calculates and applies a matched exponential window to the FID. For rho=2.0, this window doubles the line width, and is a traditional "match filter". rho values of 1.3 to 1.5 are often used as well. rho allows you to tailor the trade off between resolution and sensitivity in the transformed spectra.
Line broadening is calculated using an analytical least-squares fit to the FID. If the FID has extremely low signal to noise, the fit may fail; a message to that effect will appear on the screen and the value you have specified in lbroad will be used instead. Note that a large, narrow solvent resonance may dominate the fit. After mf, the reserved symbol lbroad is set to the value of the line broadening applied by mf.
Symbol dependence:
datsiz Number of Data Points
Symbol changed:
lbroad Line Broadening
mgv and mpv are similar to the commands gv and pv, except these two commands operate on the current matrix instead of the 1D work space.
mgv loads the value out of the matrix at one N-D point, and stores that value to a symbol. mpv stores the given value into the matrix at the specified N-D point. The matrix must be write-enabled for mpv.
See also:
gv Get Value
pv Put Value
mmp allows you to display and modify the memory map. FELIX maintains a pool of memory that can be allocated for use. The command mmp displays the size and usage for each allocated block of memory. mmp is commonly used as a diagnostic aid to help figure out what happened if something does not work properly.
The mnu command provides menuing capabilities for FELIX. The mnu operations allow macros to generate popup menus on the display device and interact with you in menu mode. Menu and control panel definitions are simple ASCII files, which you can easily customize. More detailed information on the menu manager is given in Chapter 5. Menus and control panels.
mnu bar draws a menu of items on the display. A bar menu goes across the display, while an insert menu goes down the display. The contents and size of the menu are read from the file mot_file. The location of the menu is specified in character cell units, with the upper left corner of the display being cell (x=1, y=1). No action other than drawing of the menu is performed. See Chapter 5. Menus and control panels, for a description of the contents of the menu files.
The mnu gauge command allows you to create a descriptive meter bar gauge to show the progress of any complex operation. The meter gauge visually shows any value between zero and max_value as a colored bar that grows or shrinks as cur_value changes.
In typical use, mode 1 is executed once, mode 2 is executed many times (with a different cur_value each time), and mode 3 is executed once. Note that only one gauge can be displayed at any given time. In addition, the image or picture behind the gauge should not be updated or redrawn while the gauge is displayed.
The selected item is returned in two symbols, menu and item. The menu symbol is set to the name of the file menu_file selected, or set to null if the cursor was not located on any menu. The item symbol is set to an integer specifying which item in the menu was selected, or set to 0 if the cursor was not on a menu.
Remove one menu from the display, or remove all menus if all is specified.
Draws an interactive control panel on the display, letting you see and change symbol values. This operator waits for you to select an exit button using the mouse button, and then the control panel is removed. Based on which exit button is selected, either no action is performed (button 0) or all symbols appearing in the control panel are updated (any non-zero button). The reserved symbol button is set to the button number selected. See the menu chapter for a description of the content of control panel files.
Symbol changed:
button Exit Button Number
Draws an interactive control panel on top of the tablename table, letting you see and change symbol values. This operator waits for you to select an exit button using the mouse button, and then the control panel is removed. Based on which exit button is selected, either no action is performed (button 0) or all symbols appearing in the control panel are updated (any non-zero button).
Draws a modal control panel on the display, letting you see and change symbol values. One important difference is that this control panel does not wait for you to select an exit button, but continues the execution of the macro. This widget is useful together with a multiple entry point real-time macro.
Draws a non-modal control panel on the display, letting you see and change symbol values. This control panel continues the execution of the macro without waiting for you to select an exit button. This widget is useful together with a multiple entry point real-time macro (e.g.: annotate.mac).
Both in mnu a and mnu o you can use a set of special widgets to facilitate writing real-time control macros. Here is a description of those special widgets which can be only used in these two menus:
Clicking this button executes the macro macro.
The orientation symbol can be 0 for a horizontal slider or 1 for a vertical slider. The callback symbol can define that the macro macro gets executed every time you move the slider (1) or only when you release the slider (0).
The type variable can be real (r), integer (i), or character (c).
The mnu h command allows you to change the header text of the main frame. If the mnu h 1 text command is issued then the text in the text symbol is put on the frame header. The consecutive mnu h 2 command clears up and sets back the header to the default setting of 1.
ms replaces the real part of the work space with the sqrt[(real)2 + (imag)2)] or the absolute magnitude of the data, and replaces the imaginary part of the work space with the arctan(real/imag) or the phase array of the data, in the range -180 to +180 degrees.
mul multiplies the data in the work space by the specified number. If the data in the work space is complex (datype = 1) then the multiplier may be complex. Note that if both the workspace and the parameters for this command are complex, then a complex multiplication will be carried out:
result_real = work_real * real_multiplier - work_imag * imag_multiplier
result_imag = work_real * imag_multiplier + work_imag * real_multiplier
The mul command allows you to change both the magnitude and the phase of the data in the work space.
Symbol dependence
datype Data Type
See also
add Add Number to Work
mwb multiplies the data in the work space by the data in the specified buffer. This command is commonly used after an apodization window is stored in a buffer; mwb multiplies the data in the work space by the stored window during a transform. Performing apodization by buffer multiplication saves time during lengthy multidimensional transforms.
See also
stb Store Work Space to Buffer
adb Add Work Space to Buffer
ldb Load Work Space From Buffer
Note: This chapter continues with the A_CommandRef_2.html file.
This command is used to find potential neighbor patterns for any or all patterns. This requires a peak picked 2D NOESY spectrum and its associated patterns. The nd2 command reports neighbor probabilities.
This command string defines the frequency collapse tolerance, to judge whether a candidate frequency is a new one.
minimum number of pattern frequencies with which a candidate must have NOE contacts |
|
minimum number of peaks (must be at least equal to the number of contacts) |
range of pattern frequencies to use in ppm. Only NOEs with frequencies in this range are considered. For proteins, this is the HA, HB region, possibly extended with an amide proton. |
|
This command utilizes the normalize option, which normalizes the scores for each pattern to one.
executes the neighbor detection. The peak entity for a 2D NOE spectrum should be specified |
|
all patterns, or a specific pattern, for which the detection should be carried out |
This command is used to find potential neighbor patterns for any or all patterns. This requires a peak picked 3D NOESY spectrum such as 3D NOE-NOE or 3D 15N-1H-HSQC-NOESY and its associated patterns. The nd3 command reports and stores i - i + 1 neighbor probabilities.
This command string defines the method for neighbor detection -- namely using homonuclear or heteronuclear spectrum.
This command string defines the frequency collapse tolerance, to judge whether a candidate frequency is a new one.
minimum number of pattern frequencies with which a candidate must have NOE contacts |
|
minimum number of peaks (must be at least equal to the number of contacts) |
range of pattern frequencies to use in ppm. Only NOE's with frequencies in this range are considered. For proteins, this is the HA, HB region, possibly extended with an amide proton. |
|
This command utilizes the normalize option, which normalizes the scores for each pattern to one.
range of sequential frequencies in ppm -- this is used for 3D HSQC-NOE spectrum and this is the range of the 15N frequencies |
This command string defines the frequency range for the 15N resonances in the pattern s in the case of heteronuclear neighbor detection.
This command string defines whether the program should look for reverse NOE contacts appearing in, e.g., 3D TOCSY-NOE spectra.
This command string defines the neighbor score option (values between 0 and 3), used when the reverse NOE-contact option is on.
This command string defines the type of nuclei in the pattern to use if the method is heteronuclear. You must define the nucleus1 in accordance with the range defined in command nd3 ran, and nucleus2 in accordance with nd3 seq. For example in a 3D 15N-1H-HSQC-NOESY spectrum the nucleus1 should be set to H and the range should be defined through
command for a protein and. The nucleus2 should be set to N and the range should be defined through
If a homonuclear spectrum is being used for neighbor detection, both nucleus1 and nucleus2 should be set to H.
executes the neighbor detection. The peak entity for a 3D NOE spectrum should be specified |
|
all patterns, or a specific pattern, for which the detection should be carried out |
nex defines the end for a for loop in macros. This command is only valid in macros.
no adds random noise of specified amplitude to the data in the work space. The amplitude distribution of the generated noise is normal (Gaussian) and its frequency distribution is white.
Symbol dependence:
datsiz Number of datapoints
nop performs no operation. A typical use of nop in macros involves execution of commands that are stored in symbols. For example, you could save the current window command in a symbol named window. If no window was used, the window symbol could be set to nop, which would not modify data when executed.
nor normalizes the contents of the data in the work space so a specified point defined by the data point parameter has a given value defined by the new value parameter. This command is useful for comparing integrals and relative peak heights in separate spectra.
np generates a null plot containing axes (like ip and cp) for the current region, but does not display any contours for data. np is very fast because it does not read matrix data for display. The main use of np is to establish graphics context without taking the time to draw a full plot. np is most often used prior to picking a large matrix to establish current plot context.
See also:
cp Contour plot
ip Intensity plot
old recalls the previous plot limits of 1D plots. If no previous plots were performed, the old command displays the full size of the data. For N-dimensional data, use lim -2.
Symbols changed:
first First datapoint
last Last datapoint
selects new file or appends to end of existing file: 0 = open new file for output, 1 = open existing file for appended output, 2 = open existing file for input |
opn opens a file for output or input. The default extension is .mac, but other extensions are valid as well. After opn has been used to create an output file (access_mode=0), the put command may be used in macros to put records in this file, which may contain any information you want. If the access_mode parameter is set to 1, any lines output by put will be appended to the end of an existing file. If access_mode is set to 2, the rea command may be used to read an existing file sequentially.
See also:
put Put record
cls Close output file
rea Read file
opt gets the license status of any of the Felix options. This command sets the specified symbol symbol to one if the option is licensed, and to zero if the option is not licensed to you.
To enable options that are not currently licensed, you will need a new feature in your license file. To obtain this, contact Molecular Simulations (see Appendix A, Felix Installation, in the Felix User Guide).
Licenses can be released or rerequested using the negative value for the number variable, for example:
causes the Assign license to be released if one was used by the current program (allowing other processes/users to use that feature), or alternatively check out an Assign license if there is one available in the license file.
ord is used to define the graphic representation of a matrix subspace. The default values for this command simply display the matrix dimensions in the order D1=1 (x axis), D2=2 (y axis) and D3=3 (z axis). If you wish to display the data transposed (i.e., the D2 dimension along the x axis instead of the y axis), simply exchange the order of the indices using the dim1 and dim2 parameters. For example, to display a 2D matrix transposed, enter ord 2 1. To list the current matrix order, enter lim 0.
With this command you can overlay several plots on top of each other in the Assign module. Please note that, after overlaying plots, the active plot (i.e., the one from which values can be extracted) is the last spectrum plotted. You can overlay only contour plots.
These specific options must be executed before an overlay can be carried out:
The clear option clears the overlay memory buffer; therefore anytime a new combination of spectra is to be overlaid this command has to be executed.
The set option specifies which spectrum from the database should be overlaid. You have to call this command at least two times.
The connect option allows you to set, for two spectra, which dimensions should be mutually connected after the ovc set command is executed. This is particularly useful if you want to overlay 2D planes of 3D spectra.
Finally, calling the ovc command, with no options, draws the overlay plot.
After cross peaks are picked, pd2 performs prototype pattern detection on COSY, TOCSY, and NOESY type spectra for macromolecules, or performs prototype pattern detection on COSY, TOCSY, HMQC, and HMBC type spectra for small molecules.
This command is useful only for macromolecules.
This command is useful only for macromolecules.
This command is useful only for macromolecules.
This command is useful only for macromolecules.
These command strings specify minimum numbers of contacts for COSY (cos), COSY+TOCSY (cot), and COSY+TOCSY+NOESY (ctn) type calculations, required for a frequency to be considered as a candidate, if the number of frequencies in a prototype pattern is 2, 3, 4 or more. This command is useful only for macromolecules.
This command is useful only for macromolecules.
This command is useful only for macromolecules.
minimum number of frequencies within this filter in prototype pattern |
|
maximum number of frequencies within this filter in prototype pattern |
These command strings specify the COSY peak entity, and define the method to be based on COSY spectrum.
These command strings specify the TOCSY peak entity, and define the method to be based on TOCSY spectrum.
These command strings specify the TOCSY and NOESY peak entities, and define the method to be based on TOCSY and NOESY spectra. This method is only for macromolecules.
The above command strings specify the TOCSY, COSY, and NOESY peak entities, and define the method to be based on TOCSY, COSY and NOESY spectra. This method is only for macromolecules.
The above command strings specify the HMQC and COSY peak entities, and define the method to be based on HMQC and COSY spectra. This method is only for small molecules.
The above command strings specify the HMQC and TOCSY peak entities, and define the method to be based on HMQC and TOCSY spectra. This method is only for small molecules.
The above command strings specify the HMQC, COSY and TOCSY peak entities, and define the method to be based on the HMQC, COSY and TOCSY spectra. This method is only for small molecules.
The above command strings specify the HMQC, COSY and HMBC peak entities, and define the method to be based on HMQC, COSY and HMBC spectra. This method is only for small molecules.
The above command strings specify the HMQC, TOCSY and HMBC peak entities, and define the method to be based on HMQC, TOCSY and HMBC spectra. This method is only for small molecules.
This command string executes the pd2 command for macromolecules.
This command string executes the pd2 command for small molecules.
Symbol dependence:
rprent Prototype pattern entity
pd3 performs prototype pattern detection on 3D homonuclear spectra (for example, 3D TOCSY-TOCSY or 3D TOCSY-NOESY) or on 3D heteronuclear spectra (3D 15N-1H HSQC-TOCSY, 2D 15N-1H-HSQC and 3D 15N-1H HSQC-TOCSY, 3D HCCH-TOCSY), after cross peaks are picked:
These command strings specify minimum numbers of contacts for J coupled (jco), and J coupled+NOESY (jno) type calculations, required for a frequency to be considered as a candidate, if the number of frequencies in a prototype pattern is 2, 3, 4 or more.
minimum number of frequencies within this filter in prototype pattern |
|
maximum number of frequencies within this filter in prototype pattern |
which coordinate of the seed peak to use -- usedn = 0 means not to use this coordinate as a frequency in the prototype pattern |
For heteronuclear detection you usually need to use the HN and N frequencies of the seed peaks.
which coordinate of the expansion peak to use -- usedn = 0 means not to use this coordinate as a frequency in the prototype pattern |
For heteronuclear detection you usually need to use the aliphatic H frequencies of the expansion peaks.
root frequency dimension (usually the HN dimension) necessary for heteronuclear detection methods: 3D 15N-1H HSQC-TOCSY, 2and 3D HCCH-TOCSY |
3D prototype pattern detection method -- 3D homonuclear (hom), 3D 15N-1H HSQC-TOCSY (het), 2D 15N-1H HSQC + 3D 15N-1H HSQC-TOCSY (hsq), 3D HCCH-TOCSY (hch) |
This command string specifies the method to base on the prototype pattern detection.
This command string executes the pd3 command.
Symbol dependence:
rprent Prototype pattern entity
pen lets you add additional pens to Felix. You give the RGB values that define the color and the pen number you want to refer to this new color. Using this command, you can build your own color ramps.
The color_table_size is an optional value that tells Felix how big the color map for your computer actually is.
On SGI computers running the GL version of Felix, double buffer mode limits the number of bitplanes to one half of the number you actually have. For example, an 8-bitplane machine can only support 16 colors, while a 24-bitplane machine can support 4096 colors.
This returns the rgb values for the pen number in the ired, igreen, and iblue symbols.
ph performs a phase correction on the workspace based on the current values of the reserved symbols for zero order phase correction (phase0) and first order phase correction (phase1). The workspace must contain complex data in order to perform phase correction.
Symbol dependence:
datsiz Number of datapoints
datype Data type
phase0 Zero-order phase angle
phase1 First-order phase angle
See also:
aph Autophase spectrum
rph Real-time phase
pic picks peaks in a one- or multidimensional spectrum, generates a peak list, and annotates the current display. The pic command behaves differently for 1D and 2D spectra.
pic picks 1D peaks and stores them in the database entity.
The behavior of pic is controlled by pick_mode as follows:
pic can generate peak labels on a 1D spectrum. For this application, it is recommended that you set the scale factor to 0.7, then draw (dr) the spectrum to get some empty space at the top of your current drawing. pic will label the peaks in either ppm or Hz depending on the current axis definition (set with the axtype symbol), unless pkunit is set to a number other than zero. In addition, pic will not pick any peaks smaller than the threshold value (thresh). If thresh is zero, pic sets it to 0.25 times the biggest peak. If posneg is set to 1, pic picks both positive and negative peaks.
Symbol dependence:
axtype 1D axis type
pkunit Peak pick units
thresh Peak pick threshold
level Contour level
posneg Positive/negative peak switch
Symbols changed:
picent Current peak pick entity
pic picks ND peaks and stores them in the database entity entity. The number of peaks picked is returned in symbol. The peak shapes to search for is controlled by peak_style as follows:
0=positive peaks (NOESY and TOCSY) |
When peak_style is set to one, the picker uses the values of the symbols absmg1 and absmg2 to define the x and y half widths (respectively) of a rectangle used to better find the centers of multiplet cross peaks. Picking is actually done on the convolution of the box with the absolute value of the spectrum, in effect smearing out the fine structure of multiplets into a single fat positive peak. As a rule of thumb, set absmg1 and absmg2 to about the half width of an entire multiplet cross peak in dimension 1 and dimension 2, respectively.
The mode of data storage is determined by pick_mode as follows:
1 When pick_mode is 2 or 3, the symmetry parameter controls picking of the symmetric cross-diagonal peak as well. (0=no symmetric pick, 1=do symmetric pick)
Symbol dependence:
level Contour level
hfwid1 Minimum halfwidth of the peak in points along D1
hfwid2 Minimum halfwidth of the peak in points along D2
hfwid3 Minimum halfwidth of the peak in points along D3
hfwid4 Minimum halfwidth of the peak in points along D4
mxwid1 Maximum halfwidth of the peak in points along D1
mxwid2 Maximum halfwidth of the peak in points along D2
mxwid3 Maximum halfwidth of the peak in points along D3
mxwid4 Maximum halfwidth of the peak in points along D4
maxmet Maximum definition method -- center of gravity (0) or using singular-value decomposition (1)
fixwd1 Default halfwidth along D1 if halfwidth search failed
fixwd2 Default halfwidth along D2 if halfwidth search failed
fixwd3 Default halfwidth along D3 if halfwidth search failed
fixwd4 Default halfwidth along D4 if halfwidth search failed
xpklbl Label Peaks Switch
Symbols changed:
pksent Current cross peak entity
pla redisplays a 3D object on a 3D display and allows you to manipulate it using the standard 3D user interface. There must be a current 3D object for pla to work.
pol corrects the baseline of the data in the work space using the current list of baseline points. pol uses a polynomial of the specified order for the correction. Baseline points may be defined automatically with the automatic baseline points command (abq) or defined using bas.
pol uses the value of the interval width symbol (iwidth) to minimize the effects of noise on the correction by averaging the points in the interval about each baseline point (+/- iwidth points).
Symbol dependence:
datsiz Number of datapoints
datype Data type
iwidth Interval width
See also:
abl Automatic baseline flattening
abq Automatic selection of baseline points
bas Baseline points manipulation
csp Cubic spline baseline correction
flt FLATT baseline flattening
pop causes the buffer stack head to be moved to the workspace and decreases the value of the stack depth parameter (stack).
Symbol dependence:
datsiz Number of Data Points
datype Data Type
Symbols changed:
stack Stack depth
See also:
ldb Load buffer into work space
psh Push work space onto stack
stb Store work space to buffer
xsh Exchange stack head with work space
ppm allows conversion between data point and ppm or Hz units for 1D data or for any dimension of N-dimensional data. ppm uses the information entered using ref (1D) or rmx (ND) and gives easy access to shift information
pattern number to store the residue probabilities with, if none is defined the probabilities will just printed out to the text window |
This command uses the Grzesiek-Bax method (Grzesiek and Bax 1993) to calculate residue type probabilities from the Ca and Cb chemical shifts. This command either stores the result with the pattern if the pattern number (pattern) is given, or prints out the result to the text window.
prf puts a format description (FORTRAN style) for printing variables (symbols) into a string (symbol). For example:
prints an integer, then text, then a real number, and then the quoted text to the variable (symbol) result.
The allowed format directives are:
i integer
f float
e scientific notation float
a character string
x space
t tab
Note: Each variable in the list should have a specific formatting statement. For example. you cannot use 2(f7.3) in the format statement -- you must instead use f7.3,f7.3.
ps replaces the real part of the data in the workspace with [(real)2 + (imag)2], or the power spectrum, and sets the imaginary part to the phase angle.
This command can be used to find potential matchings of patterns assigned to residue types onto the sequence of an unbranched biomacromolecule. The neighbor detection commands (nd2 or nd3 or the supported macros) and the residue type identification command (prb or the supported macros) should be run before using the psa command.
This command stores and sort assignments or prints them as they are determined.
This command string executes the psa command and stores the resulting stretches in the stretch entity.
psh causes the contents of the data in the workspace to be pushed onto the buffer stack. The stack depth symbol (stack) is incremented and the contents of the data in the workspace remain unchanged. This command is useful for saving some data temporarily, or for displaying more than one spectrum at a time using the draw command (dr).
Symbol dependence:
datsiz Number of datapoints
datype Data type
Symbols changed:
stack Stack depth
See also:
ldb Load buffer into work space
pop Pop display stack
stb Store work space to buffer
xsh Exchange stack head with work space
pso removes a solvent signal from the time domain data. The solvent signal is approximated by calculating the mean value of every window points and fitting a polynomial of order order to the mean values. The resulting function is subtracted from the time domain data in work. This command performs well when the solvent frequency is close to zero.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
cnv Time-domain convolution
lps Solvent suppression using linear prediction
puf takes a format description (FORTRAN style) for printing variables (symbols) and stores it in a file which was opened previously by the opn command. This command is similar to the put command but it allows formatting. For example:
prints an integer, then a text, then a real number, and then the quoted text to the previously opened file.
The allowed format directives are:
i integer
f float
e scientific notation float
a character string
x space
t tab
Note: Each variable in the list should have a specific formatting statement. For example, you can not use 2(f7.3) in the format statement -- you must instead use f7.3,f7.3.
The pur command purges the symbol list, causing user-defined symbols to be deleted. The symbol can be wildcarded:
which purges all variables having the first three letters "abc".
put writes one line of text, defined by the parameter text, to the current output file (opened using opn). put can be used only within macros, and is useful for building new macros within a running macro. The text string will be subjected to symbol value replacement. To prevent symbol substitution within the text, precede the ampersand (&) with an exclamation point (!). The exclamation point (!) will prevent symbol replacement due to the ampersand (&), and the exclamation point (!) is then deleted from the output. Using the special string %t within the text creates a tab within the file.
See also:
opn Open record
cls Close record
pv puts the specified value into the specified data point in the work space. If the point number is outside the range between 1 and the frame size (frsize), no action is taken. If the work space is complex (datype=1), then imaginary_value is put into the imaginary part of the work space point.
This command can be used to automatically assign peaks after the spin systems are assigned to specific atoms.
This command string executes the pxp peak autoassignment command using the entity peak table.
qsb multiplies the data in the work space by a skewed (or weighted) sinebell window. The skew, if less than one, skews the window to the left. If the skew is greater than one, the window function is skewed to the right.
Symbol dependence:
datsiz Number of datapoints
See also:
sb Sinebell window
ss Sinebell squared window
qss Skewed sinebell squared window
qss multiplies the data in the work space by a skewed (or weighted) sinebell squared window. The skew, if less than one, skews the window to the left. If skew is greater than one, the window function is skewed to the right.
See also:
ss Sinebell squared window
sb Sinebell window
qsb Skewed sinebell window
ra reads ASCII 1D data files produced by the write ASCII (wa) command. This command provides you with a means of transferring data between unlike hardware or different programs.
optional parameter -- specifies which pdata/process_#/proc(n)s files to use. If omitted it will search in for pdata/1... pdata/9 directories and whichever is found first will use that. |
rb reads an FID from file into the 1D work space. rb can read Bruker files written on models AMX and newer. It is also important but not essential that the acqus... and pdata/../procs... files are present together with the ser or fid file, since the header parameters are read and used in Felix.
Symbol dependence:
frsize Frame size
Symbols changed:
datsiz Number of datapoints
datype Data type
status Error status
axtype Axis type
refsh Reference shift
refpt Reference point
phase0 Zero-order phase angle
phase1 First-order phase angle
sfreq Spectrometer frequency
swidth Spectrum width
See also:
cl Close file
re Read file (old format)
rn Read file (new format)
rf Read Felix for windows file
rv Read Varian file
rj Read JEOL file
ra Read ASCII
re reads a data record from the specified file. The default file extension for the read command is .dat, therefore the extension does not need to be entered unless it differs from the default extension.
Felix uses the same file type for 1D and 2D data. However, 2D datafiles contain more than one record. The data will therefore be read sequentially by issuing successive read (re) commands. To re-examine a data record after it has been read, the close command (cl) must be used to close the current data file and to re-position the record pointer to the beginning of the file.
Symbol dependence:
frsize Frame size
Symbols changed:
datsiz Number of datapoints
datype Data type
status Error status
axtype Axis type
refsh Reference shift
refpt Reference point
phase0 Zero-order phase angle
phase1 First-order phase angle
sfreq Spectrometer frequency
swidth Spectrum width
See also:
cl Close file
rn Read file (new format)
rb Read Bruker file
rf Read Felix for windows file
rv Read Varian file
rj Read JEOL file
ra Read ASCII
rea reads the next record from the current file opened using opn 2. The text of the record will be placed in the meta-string "$str".
See also:
opn Open ASCII file
cls Close ASCII file
sub Sub-string extraction
rec draws a rectangle having opposite corners (x0,y0) and (x1,y1). The color of the line is set by defining the symbol anncol. The coordinates may be specified in a variety of units as specified by annunt.
Symbol dependence:
anncol Annotation color
annunt Annotation units
See also:
ann Annotate plot
lin Line annotation
red reduces a complex spectrum to a real one by discarding the imaginary part of the data in the workspace. The reduce command is used to convert a complex spectrum to a real spectrum.
Symbol dependence:
datsiz Number of datapoints
datype Data type
Symbols changed:
datype Data type
ref defines the shift reference for 1D spectra. You can also reference a spectrum using the menus. For multidimensional spectra, use the rmx command.
Symbol dependence:
axtype Axis type
Symbols changed:
refpt Reference point
refsh Reference shift
ret returns control from a called macro to the calling macro.
See also:
cal Macro call
exr Execute macro and return
rev causes the data in the workspace to be reversed by swapping the data point values of 1 and 1024; 2 and 1023; 3 and 1022; and so on. When using this command, it makes a difference whether the data in the workspace is real or complex since, for the complex case, reversal will be pairwise.
Symbol dependence:
datsiz Number of datapoints
rf reads an FID from the Felix for Windows file_name into the 1D work space.
Symbol dependence:
frsize Frame size
Symbols changed:
datsiz Number of datapoints
datype Data type
status Error status
axtype Axis type
refsh Reference shift
refpt Reference point
phase0 Zero-order phase angle
phase1 First-order phase angle
sfreq Spectrometer frequency
swidth Spectrum width
See also:
cl Close file
re Read file (old format)
rb Read Bruker file
rv Read Varian file
rn Read file (new format)
rj Read JEOL file
ra Read ASCII
rft assumes the contents of the work space to be real, and performs an in-place real Fourier transform. rft turns a real vector of length datsiz into a complex vector of length (datsiz/2).
Symbol dependence:
datsiz Number of datapoints
datype Data type
Symbols changed:
datsiz Number of datapoints
datype Data type
See also:
ft Fourier transform
ift Inverse Fourier transform
bft Bruker transform
hft Hilbert transform
rj reads an FID from the JEOL file_name into the 1D work space. rj can read JEOL files collected with Alpha or Lambda systems.
Symbol dependence:
frsize Frame size
Symbols changed:
datsiz Number of datapoints
datype Data type
status Error status
axtype Axis type
refsh Reference shift
refpt Reference point
phase0 Zero-order phase angle
phase1 First-order phase angle
sfreq Spectrometer frequency
swidth Spectrum width
See also:
cl Close file
re Read file (old format)
rb Read Bruker file
rf Read Felix for Windows file
rn Read file (new format)
rv Read Varian file
ra Read ASCII
rm reads the macro file defined by the file_name parameter into the macro work space. All macros must have the default .mac extension. Once the macro is in the macro work space, it can be executed (ex) or listed (lm).
Symbol dependence:
macpfx Macro prefix
Symbols changed:
macfil Current macro file
rmx sets shift reference information for one dimension of a matrix. This is similar to the ref command used for 1D data. A matrix must be opened before referencing. The reference information is stored permanently in the matrix file.
rmx may also be used to extract reference information from a matrix by using a negative dimension. The reference information corresponding to the above usage of rmx is loaded into the user symbols sym1 through sym6.
rn reads a file into the 1D work space. rn can read new format files written on hardware with a different byte order and transferred over a network.
Symbol dependence:
frsize Frame size
Symbols changed:
datsiz Number of datapoints
datype Data type
status Error status
axtype Axis type
refsh Reference shift
refpt Reference point
phase0 Zero-order phase angle
phase1 First-order phase angle
sfreq Spectrometer frequency
swidth Spectrum width
See also:
cl Close file
re Read file (old format)
rb Read Bruker file
rf Read Felix for Windows file
rv Read Varian file
rj Read JEOL file
ra Read ASCII
rph performs real-time display of data allowing one to manipulate zero-order and first-order phase corrections as well as the pivot point in real time. Typical use involves first setting a pivot point (by pressing the <Shift> key and the right mouse button) near one end of the spectrum: adjusting the first-order phase will not affect the phase of the spectrum at the pivot. Zero order phase is then adjusted to give correct phases near the pivot, and first-order phase is adjusted for correct phase furthest from the pivot.
rph allows expansion of regions using the expand button, and return to full spectrum using the full button. The sensitivity of the slider bars can be adjusted using the finer and coarser buttons. The quit and keep buttons allow you to exit rph, while ignoring or applying the phase correction.
Symbol dependence:
datsiz Number of datapoints
datype Data type
Symbols changed:
phase0 Zero-order phase angle
phase1 First-order phase angle
rpl is a manual version of pol that incorporates a real-time display. rpl allows you to adjust the polynomial coefficients of each order and displays a baseline function along with the spectrum to be corrected. This imitates the behavior of the Bruker knob-based polynomial baseline correction.
See also:
pol Polynomial baseline correction
rv reads an FID from the Varian file_name into the 1D work space. rv can read Varian fid files together with the procpar file collected under VXNMR 5.0 or newer.
Symbol dependence:
frsize Frame size
Symbols changed:
datsiz Number of datapoints
datype Data type
status Error status
axtype Axis type
refsh Reference shift
refpt Reference ppoint
phase0 Zero-order phase angle
phase1 First-order phase angle
sfreq Spectrometer frequency
swidth Spectrum width
See also:
cl Close file
re Read file (old format)
rb Read Bruker file
rf Read Felix for Windows file
rn Read file (new format)
rj Read JEOL file
ra Read ASCII
sar provides subcommands related to the Autoscreen module for SAR by NMR. Execution of this set of commands requires the Autoscreen license.
sar ini uses the values of these symbols:
pksent Entity name of the cross peaks in the database.
mindis1, maxdis1 Lower and upper limits of peak displacements in the D1 dimension.
mindis2, maxdis2 Lower and upper limits of peak displacements in the D2 dimension.
h1fac, n2hfac Scale factors for 1H and 15N chemical shifts.
thrmet Options for threshold method.
sarntp Number of sample points used to determine threshold automatically.
thrval User-defined threshold.
xpktyp Selection mode for peak picking.
maxmet Local maximum method for peak picking.
widop Option on whether or not to use peak width when matching peaks.
hgtop Option on whether or not to use peak height when matching peaks.
sarmsh Minimum similarity in peak shape required to match peaks.
scomet Method for searching a best match between the test and control peaks.
sarcpu The maximum CPU time (in seconds) allowed for a depth-first search.
ucpfit Option on whether or not to fit unmatched control peaks to the test spectrum.
sarnmw Penalty of an unmatched control peak.
utpopt Selection method for unmatched test peaks
utpsgm Number of standard deviations tolerated when filtering unmatched test peaks.
sarutp Penalty of an unmatched test peak.
scomat Filename of the score matrix.
scorent Entity name of the scores in the database.
sb performs a sinebell multiplication of the data in the work space using a function specified by the size and shift parameters. If no parameters are entered, the global parameter size (datsiz) is substituted for the size parameter and a phase shift of zero degrees is used. The sinebell window function yields good results for absolute magnitude spectra.
Symbol dependence:
datsiz Number of datapoints
See also:
ss Sinebell squared window
qsb skewed sinebell window
qss skewed sinebell squared window
sca is used to control the appearance of multidimensional data displays. For example, if sca 2 3 is entered, all plots will display dimension 2 scaled three times larger than normal. The default scale factor for all dimensions is one.
If the scale_factor is set to -1 then the plot is dynamically scaled, which means that the aspect ratio is discarded, and the plot fills out the available frame.
returns the current scaling in scale_factor_variable if the negative dimension is used for the dimension.
seg controls the creation, scaling, and display of segmented integrals on 1D spectra. The symbol segint switches on and off the automatic display of segmented integrals on 1D plots. The segment definitions are stored in a DBA entity named by the symbol
segent. Specifying lowpt as -1 enables a rubber band box cursor for adding and normalizing segments.
Symbol dependence:
segent Segments entity
sep converts data consisting of alternating real and imaginary parts into data containing separate real and imaginary parts. All data within Felix is processed in alternating mode. sep is useful for recovering imaginary parts of hyper-complex spectra for phasing after initial transformation. sep defines the data type to real, (datype=0) and defines the data size to two times the number of complex points.
Symbols changed:
datsiz Number of datapoints
datype Data type
See also:
alt Alternating real and imaginary
set simply assigns the specified value to all points in the work space. This command is useful for looking at the shape of window functions. For example, set 1 sets the data in the work space to one. The desired window commands can then be issued, performing a window multiplication. The dr command can then be issued to draw the applied function in the graphics display to see what it looks like. If the work space is defined as being complex (datype=1), the set command can be used to define a complex value by specifying both the real and imaginary parameters.
Symbol dependence:
datsiz Number of datapoints
datype Data type
shl shifts the data in the work space left by the number of points specified by the points parameter. Data values of zero are added to all points that lie to the right of the shift.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
shr shift right
ssh signed shift
csl circular shift left
csr circular shift right
csh circular signed shift
shr shifts the data in the work space right by the number of points specified by the points parameter. Data values of zero are added to all points that lie to the left of the shift.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
shl Shift left
ssh signed shift
csl circular shift left
csr circular shift right
csh circular signed shift
smo performs a binomial smooth on the data in the work space by subjecting the data to a three-point smooth with binomial weighting. smo 2 is equivalent to a five-point binomial smooth while smo 3 is equivalent to a seven-point binomial smooth, and so on. Repetitive binomial smoothing is, in the limit of large numbers for the parameter times, equivalent to applying Gaussian convolution.
See also:
flf FaceLift baseline correction
sp produces a stack plot of the current region on the defined graphics device (display or plotter). The command sp uses the reserved symbols deltax for stack plot, deltay for stack plot, rowinc for row increment, and cutoff for peak height cutoff. These symbols control the appearance of the plot. sp produces plots that have a 3D appearance.
sp autoscales the peak heights. The autoscaling can be disabled by setting the reserved symbol absint to one. In this case, sp uses the scaling factor calculated for the most recent autoscaled cp, ip, or dr command.
Symbol dependence:
deltax Delta X
deltay Delta Y
rowinc Row increment
bigpt biggest point
scale scale factor
Symbols changed:
disply Current display type
sqz compresses matrices so that any point whose value is less than threshold is not included in the new squeezed matrix. Squeezed matrices are read-only, yet it is possible to define reference information using rmx after squeezing.
srv can be used to set any range of the data in the work space to a single value. Typically, the srv command is used to generate window functions that avoid truncation errors while minimally altering spectral intensities. For example, the following series of commands:
defines a window equal to one for the first 600 points, which then drops smoothly to zero from point 600 to point 700, as a 90 degree shift sinebell function.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
set Set workspace to value
ss performs a sinebell squared multiplication of the data in the work space using the parameters specified by size and shift. If these parameters are not entered, the global parameter data size (datsiz) with a phase shift of zero degrees is used. The ss command is a very good window function for apodizing absolute magnitude spectra.
See also:
sb sinebell window
qsb skewed sinebell window
qss skewed sinebell squared window
ssh shifts the data in the work space to the left or right a certain number of points specified by [n1 - n2]*scale. Negative values shift the spectrum left while positive values shift the spectrum right. The ssh command can be used for tilting spectra where the scale parameter is usually set to the ratio of the w1 to w2 digital resolution.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
shr shift right
shl shift left
csl circular shift left
csr circular shift right
csh circular signed shift
ssp generates a synthetic spectrum from peak parameters in the peaks entity peaks. The generated synthetic spectrum retains the data type (real or complex) of the original data. This is useful following peak fitting (fit) to generate the modeled spectrum.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
pic pick peaks
fit fit peaks to spectrum
The ste command picks the peaks using example peaks in the xpk:example entity. It uses the current matrix limits and the current contour threshold to pick the peaks. The previous contents of the peak entity are preserved.
Symbol dependence:
cosami minimum match factor
tresnb neighbor threshold
minbok minimum number of neighbor points within the search limits
above the threshold
locsiz1 search size from maximum along d1 in points
locsiz2 search size from maximum along d2 in points
locsiz3 search size from maximum along d3 in points
locsiz4 search size from maximum along d4 in points
maxmet method to locate the maximum (0=rough maximum, 1=interpolation, 2=center of gravity)
trsint peak box threshold
facint hump tolerance factor
nextra extra points to increase by the peak box
outlev output level (0=quiet, 1=low, 2=medium, 3=high)
stb copies the contents of the work space into the specified buffer. The previous contents of the buffer are overwritten during the write process. The data in the work space and the stack depth parameter (stack) remain unchanged. The stb command is useful for temporarily saving spectral data.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
psh push workspace onto stack
ldb load work space from buffer
pop pop the display stack
xsh exchange stack head with work space
sto stores the work space to the specified vector in the matrix. For example, sto 0 1 stores to the vector along D1 that passes through point 1 of D2; and sto 1 0 stores to the vector along D2 that passes through point 1 of D1. sto must be given exactly one parameter that is zero. You can think of the zero as specifying the dimension along which the vector is loaded, and the other parameters locating the vector position in all other dimensions.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
loa store vector to matrix
swb store work space to bundle
str provides a variety of string manipulation operators. As a group, these let you perform almost any desired action involving character strings. To include blank characters into a string, enclose it in single quotes.
For use with the rea command, string may always be the meta-string $str to denote the line most recently read from an ASCII file.
Return the length of the given string. The result is an integer greater than zero.
Return a substring of the given string. Specify the first and last character locations wanted. The result is a string. This command is identical to SUB.
Return the starting position in the given string where the first instance of the substring was found. Returns zero if the substring was not present in the given string. The result is an integer.
Determines whether a wildcard string matches the given string. A valid wildcard string is of the form: abc*, *abc, *abc*. The result is an integer, where: 0 = not a match 1 = a match.
Parse the given string into words, based on blanks and any other given delimiters. Each word in the string is stored in a symbol, and the total number of words is stored in a symbol.
For example, the command line:
yields the following symbols and symbol values:
parses based on blanks and the extra delimiters `().,' to yield:
Note that any ASCII characters may be used as delimiters. The blank is always a delimiter.
Determines whether a string exactly matches the given string. The wildcards (*) are taken literally. The result is an integer, where: 0 = not a match 1 = a match.
sub extracts a sub-string from the symbol text based on the symbols begin and end and stores it into symbol. This command can be used after the rea command to extract portions of text lines from an ASCII file. The meta-string $str is used for text in this context.
See also:
rea Read ASCII text from file
swb stores the contents of the data in the workspace into the vector last accessed by the load workspace from bundle command (lwb). Before using the swb command, you must use the bundle command (bun) to define the matrix as a bundle of vectors along a specified dimension. swb must follow lwb, as lwb increments the vector count in the matrix.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
bun set bundle mode
lwb load workspace from bundle
sys puts you in touch with the command interpreter of the operating system. This command enables you to do most system operations, with a few exceptions. Since this is accomplished by spawning a subprocess, some commands will affect only the subprocess and not the Felix process itself.
scaling of text -- fixed (0), according to Y size of plot (1), according to X size of plot (2), according to both sizes (3) |
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centering -- left justify (0), center point (1), right justify (2) |
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tex draws text with its origin at the point (x0,y0) (optionally z0 and a0 if strip plot of a 3D or 4D matrix). The size of the text is set by defining the text size (annsiz) and the angle is set with the text angle symbol (annang). The color of the line is defined with the text color symbol (anncol). All coordinates are normalized device coordinates. tex can draw the full ASCII character set. However, you may not include the special characters "&" and ";" in the tex command within a macro. For a Greek character, use the gre command.
Symbol dependence:
anncol annotation color
annunt annotation units
annang annotation angle
annsiz annotation text size
slant annotation text slant
thick annotation text thickness
See also:
ann Annotate plot
gre Greek text annotation
til allows 2D subspaces of N-dimensional data to be plotted in segmented tiles with intervening data omitted. This permits detailed comparison of cross peaks from several parts of the spectrum at once.
There are three methods for generating a tile display. You can tile a cross peak and see all other peaks that align with the selected peak. You can tile a set of spins, and see the spin system based on the assigned shifts. Lastly, you can tile a pattern file containing pairs of atom names and see the spin system based on the assigned shifts.
To build a tile entity automatically from one cross peak, use til make. To display the data in these tiles, use til on. To eliminate one row or column of tiles, use til reduce. To return to normal non-tiled spectral displays, use til off. You can generate any tile display you want by creating your own tile entity, then turning tiles on and specifying the new tile entity.
To build a tile entity from a single cross peak use the peak item# as a center, and find all peaks that overlap this peak in both dimensions. When correlation is non-zero, eliminate those peaks whose line shape correlation with the specified peak is below correlation. Finally, make tile segments for each of these peaks. Each segment is tile_size points in size, or sized to the peak footprint if tile_size is zero. The tile segments are stored in the DBA entity tile_entity.
The above example builds a tile based on an atom name. Use an atom name specifier (may include *) to find all matching names in the spins entity that have assigned shifts defined in the shift entity. Build tile segments from each chemical shift for each of these spins. Each segment is tile_size points in size, or will be sized to the line width of each spin if tile_size is zero. The tile segments are stored in the DBA entity tile_ent.
The above example builds a tile entity from a pattern file. This is very similar to til atoms, except the spin names are extracted from an ASCII file that contains two spin names per line. A typical pattern file can contain expected NOE or J interactions between a set of spins, where each line specifies the names of two spins expected to interact.
This operator turns tiling on and off. You can switch back and forth between a normal contour plot and a tile plot based on a specified tile entity.
This operator combines overlapping tiles based on the overlap variable.
The above example reduces a tile display by removing one tile segment from one dimension. This has the effect of removing one entire row or column of tiles from the display. If dimension is -1, then a crosshair cursor is enabled to select the tile row or column to reduce by clicking on its axis label.
This operator allows you to make 2D strips from a 3D data set where each strip can be taken from a different plane.
This command allows you to query the cursor position with respect to a strip plot -- specifically, which strip plot the cursor pointed to.
Symbols changed:
disply Current display type
tim provides some basic timer abilities. Most notably, you can time long processing macros.
tm multiplies the data in the work space by a trapezoidal window that rises from zero at the first point up to one at p1, is equal to one from p1 to p2, and falls to zero from p2 to p3.
ty types the one line of text that follows it. ty can be used only within macros, and is useful for writing tutorial macros or for generating messages so you can monitor the execution of a macro.
tyf provides a way to put a large amount of text to the user with one command.
tym types the one line of text that follows it to the Motif text widget at the bottom of the main Felix window. tym can be used only within macros, and is useful for writing tutorial macros or for generating messages so you can monitor the execution of a macro. Be aware that this command can slow down macro execution quite drastically.
unf produces a symmetric vector in the workspace by creating the mirror image of a spectrum and placing it on the right side of the current 1D vector. The unf command is almost the inverse of the fold work command (fol). The data size is doubled.
Symbol dependence:
datsiz Number of datapoints
datype Data type
Symbols changed:
datsiz Number of datapoints
Types the version number and release date to the text frame. The reserved symbol,
flxver, is set to the version number as an integer, i.e., 230 for version 2.3.
vol extracts volumes of each cross peak in the database entity peaks from the current matrix. The footprint for each cross peak is stored in the DBA peak entity. The vol command stores cross peak volumes into the specified slot of the DBA volume entity. Volumes can be output in ASCII using standard DBA capabilities, or used by the md (model data) command.
Symbol dependence:
hafwid half width factor
wa will write an ASCII 1D data file to the disk with the specified name file_name. The wa command is the easiest way to transfer spectra to an alien program.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
ra Read ASCII data file
wr write data file (old format)
wn write data file (new format)
wai causes the program to wait for the specified number of seconds. The wai command is useful for causing delays in tutorials and may also be used to allow other users of your computer access to the processor while a multidimensional transform is being performed.
wm writes the macro from the macro work space to a .mac file.
Symbol dependence:
macpfx Macro prefix
See also:
rm READ MACRO
LM LIST MAcro
wn writes the contents of the work space to the specified file name. Files written using wn may be read after being transferred to hardware of differing byte order. wn allows you to write multiple 1D vectors into one file.
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
wr write data file (old format)
rn read data file (new format)
wr writes the data in the current work space to a disk file with the specified name file_name. Subsequently, the data file can be retrieved using the read file command (re).
Symbol dependence:
datsiz Number of datapoints
datype Data type
See also:
wa Write ASCII data file
wn write data file (new format)
re read data file (old format)
xpa uses information in the shifts and spins entities to generate parent names in an existing cross peak entity. For each cross peak in the peaks entity, xpa searches for the most appropriate parent with a shift defined in the shifts and spins entities. The parent name from the spins entity will be added to the cross peak entity as well as a spin pointer. If a parent name already exists in the cross peak entity, the name will not be changed.
See also:
xps cross peak-generated spins and shifts
xpk provides operators for adding, deleting, and manipulating cross peak information stored in the database. Each operator acts on a single cross peak item that may be specified explicitly by item number or by selecting a cross peak using the crosshair cursor (item = -1). Each operator and its function are described explicitly below.
Symbol dependence:
hafwid cross peak half width factor
See also:
xpl cross peak list manipulations
This operation finds the single cross peak in the specified cross peak entity peaks that is closest to the designated N-dimensional point location. Specifying a D1 location of -1 enables a crosshair cursor that may be used to select a location graphically. The selected point location must lie inside the cross peak footprint. The result stored in symbol is the item number of the closest cross peak, or zero if no peak footprint touches the specified location.
This operation allows you to manually add a single cross peak to the peaks entity. xpk add enables a crosshair cursor which is then used to locate the center of the desired cross peak, then a rubber box which is used to define the shape of the desired footprint. In contrast with pic, this operator does not reference the data values, and allows you to define footprints in regions of noise for the purpose of defining base intensities or noise levels. The new cross peak footprint is displayed in red.
xpk delete deletes a single peak item from the cross peak entity peaks. The explicit item number may be specified or the peak may be selected graphically by specifying an item number of -1. The deleted peak is then overdrawn in black.
This operator allows you to edit a cross peak footprint in the peaks entity. A single cross peak is selected by using the crosshair cursor. The selected cross peak is displayed in green. The mouse is then used to edit the cross peak footprint in one of two ways. The footprint center may be moved using a click-and-drag of the mouse, while the size of the footprint remains the same. If the mouse button is pressed near a cross peak corner, movement of the mouse adjusts the size of the footprint in both dimensions. Both modes terminate when the mouse button is released. The old footprint is then redrawn in black, and the new footprint is drawn in red to show the edited result. The item number of the selected peak (or zero if no peak is selected) is stored in
symbol.
xpk name inserts a cross peak parent name into the peaks entity. The cross peak may be selected explicitly by item number or graphically using a crosshair cursor if item is -1. The parent name should obey a nomenclature which is consistent with all structures and assignment libraries. The name null is used to indicate an unknown parent.
This operator integrates the intensity within the cross peak footprint. The cross peak may be selected explicitly by item number or graphically using a crosshair cursor if item is -1. The intensity of each data point within the cross peak footprint is summed and returned in symbol1. The item number of the selected peak is returned in symbol2 (zero if no peak was selected).
xpk correlate calculates a correlation coefficient between two cross peaks based on either line shape projections or position. The dimension along which the correlation is calculated is automatically chosen to be the dimension along which the peaks are closest. The result will be in the range 0.0 to 1.0, with zero indicating no correlation and one indicating perfect correlation.
xpl provides operators for creating item lists of cross peaks. For general information about lists, see Chapter 7, The Database. Each of the following operators can be constructed from a set of DBA list commands and a small macro, but they are provided in the xpl form for simplicity and faster execution when dealing with lists of cross peaks.
Symbol dependence:
hafwid cross peak half width factor
frsize frame size (biggest list size)
nframe number of buffers (number of lists)
See also:
cfg configure memory
dba database facility
xpk cross peak manipulation
xpl box makes a list of all peaks inside an N-dimensional box. The center point of a peak must be within the specified box for the cross peak to be added to the list. The first form of this operator uses explicit low and high limits for all matrix dimensions to define the N-dimensional box. If lo1 is zero, the current plot limits are used to define the box. If lo1 is -1, a rubber box cursor is enabled allowing you to define the box graphically. The number of cross peaks selected for the list is returned in symbol.
xpl touch_box makes a list of all peaks inside an N-dimensional box. Any portion of a peak must be within the specified box for the cross peak to be added to the list. The first form of this operator uses explicit low and high limits for all matrix dimensions to define the N-dimensional box. If lo1 is zero, the current plot limits are used to define the box. If lo1 is -1, a rubber box cursor is enabled allowing you to define the box graphically. The number of cross peaks selected for the list is returned in symbol.
xpl inside_box makes a list of all peaks inside an N-dimensional box. The entire footprint of a peak must be within the specified box for the cross peak to be added to the list. The first form of this operator uses explicit low and high limits for all matrix dimensions to define the N-dimensional box. If lo1 is zero, the current plot limits are used to define the box. If lo1 is -1, a rubber box cursor is enabled allowing you to define the box graphically. The number of cross peaks selected for the list is returned in symbol.
This operator builds a list of all peaks that touch an N-dimensional point. The peak footprint must include the specified point to be included in the list. The first form of the operator specifies explicit data points in all dimensions. Alternatively, if pt1 is
-1, a crosshair cursor is enabled allowing you to specify the point graphically. The number of selected peaks is returned in symbol.
xpl line builds a list of all cross peaks that touch a specified line. A line is defined in this context as an (N - 1) dimensional subspace of the matrix. This would be a line in a 2D matrix, a plane in a 3D matrix, and a rectangular prism in a 4D matrix. All cross peaks that touch point pt along dimension dimen are included in the specified list. The first form of the line operator specifies an explicit dimension and point. The second form specifies a single point, and selects cross peaks that touch that point along any dimension. Alternatively, you can specify dimen as -1 to enable a crosshair cursor and select the point graphically. In this case cross peaks are selected that touch either line of the crosshair cursor. The number of selected peaks is returned in
symbol.
This operator builds a list of all cross peaks whose centers lie within the specified range between lo_pt and hi_pt along the selected dimension dimen. The number of selected peaks is returned in symbol.
xpl name builds a list of all cross peaks whose parent name along dimension dimen matches name. If dimen is zero, the list will include any cross peak having a parent matching name along any dimension. A wild card (*) may be used in name to select partially defined parents.
This subcommand makes a list of peaks that align with a frequency list. Each peak in the list will have its center in that dimension within resolution of a frequency in that frequency list.
Using a dim of zero will give all peaks that align with a frequency in any dimension; while a dim of minus one will give only the peaks that align with a frequency in all dimensions.
The number of peaks in the list is returned in symbol.
This subcommand makes a list of peaks that align with the frequencies of a pattern from the Assign database. Each peak in the list has its center in that dimension within resolution of a frequency in that pattern. You can use either generic shifts of the frequencies (spectrum_id = 0) or a specific spectrum's shifts.
Using a dim of zero will give all peaks that align with a frequency in any dimension; while a dim of minus one will give only the peaks that align with a frequency in all dimensions.
The number of peaks in the list is returned in symbol.
This subcommand makes a list of peaks that align with the frequencies of a protopattern from the Assign database. Each peak in the list will have its center in that dimension within resolution of a frequency in that protopattern.
Using a dim of 0 gives all peaks that align with a frequency in any dimension; while a dim of -1 gives only the peaks that align with a frequency in all dimensions.
The number of peaks in the list is returned in symbol.
This subcommand makes a list of peaks that align with the frequencies of the frequency clipboard in the Assign database. Each peak in the list will have its center in that dimension within resolution of a frequency in the clipboard.
Using a dim of 0 gives all peaks that align with a frequency in any dimension; while a dim of -1 gives only the peaks that align with a frequency in all dimensions.
The number of peaks in the list is returned in symbol.
This subcommand makes a list of peaks that have their assignment pointers identical to the target assignment_pointer in the required dimension.
Using a dim of 0 gives all peaks that have that pointer in any dimension; while a dim of -1 gives only the peaks that have that pointer in all dimensions.
The number of peaks in the list is returned in symbol.
xpl pb makes a list of all peaks inside an N-dimensional box defined in ppm. The center point of a peak must be within the specified box for the cross peak to be added to the list. It is necessary to define the explicit low and high limits in ppm for all matrix dimensions to define the N-dimensional box.The number of cross peaks selected for the list is returned in symbol.
xpl tp makes a list of all peaks inside an N-dimensional box defined in ppm. Any portion of a peak must be within the specified box for the cross peak to be added to the list. It is necessary to define the explicit low and high limits in ppm for all matrix dimensions to define the N-dimensional box. The number of cross peaks selected for the list is returned in symbol.
xpl ip makes a list of all peaks inside an N-dimensional box defined in ppm. The entire footprint of a peak must be within the specified box for the cross peak to be added to the list. It is necessary to define the explicit low and high limits in ppm for all matrix dimensions to define the N-dimensional box.The number of cross peaks selected for the list is returned in symbol.
This operator builds a list of all peaks that touch an N-dimensional point defined in ppm. The peak footprint must include the specified point to be included in the list. It is necessary to define explicit data points in ppm in all dimensions. The number of selected peaks is returned in symbol.
xpl pl builds a list of all cross peaks that touch a specified line. A line is defined in this context as an (N - 1) dimensional subspace of the matrix. This would be a line in a 2D matrix, a plane in a 3D matrix, and a rectangular prism in a 4D matrix. All cross peaks that touch point ppm along dimension dimen are included in the specified list. It is necessary to define explicit dimension and point in ppm. The number of selected peaks is returned in symbol.
This operator builds a list of all cross peaks whose centers lie within the specified range between loppm and hippm along the selected dimension dimen. The number of selected peaks is returned in symbol.
new/append switch: 0=build new spins and shifts entities, 1=append to existing spins and shifts entities |
The xps command provides a mechanism to build spin and shift entities from cross peak parent assignments contained in the cross peak entity. The cross peak entity allows two different ways of assigning a parent. One simply involves entering a text parent name into the cross peak item defining a parent along a given dimension. The other involves setting a parent pointer that refers to an item in a spin's or parent's entity. The pointer mechanism is favored for assignment purposes, since the parent name actually only occurs in one place, and points to all its cross peak "children" in all experiments.
Since spin and shift entities are required for back calculation, this command allows you to generate these entities from a cross peak entity with explicit parent names. For each unique parent name in the specified peaks entity, xps will add this name to the spins entity and the shift and line width information to the shifts entity. If the same parent name occurs in more than one cross peak, the shift and line width information from all cross peak children of that parent are averaged together. Any significant discrepancies are reported, allowing you to screen these for possible mis-assignments.
See also:
bck back calculation
xpa cross peak assignments from spins and shifts
xsh exchanges the data in the work space with the buffer stack head. The xsh command reverses the position of the lower two plots drawn with the draw command (dr).
Symbol dependence:
datsiz number of datapoints
datype data type
stack stack depth
See also:
ldb load buffer into work space
stb store work space into buffer
pop pop buffer stack
psh push work space onto buffer stack
The simulated annealing assignment commands consist of functions that: 1) find spin systems (prototype patterns) in TOCSY and optionally COSY and optionally 1H-13C-HSQC cross peak sets using simulated annealing algorithm, 2) fit spin systems (patterns) with residue probabilities and neighbor probabilities to the sequence using simulated annealing.
The command finds specified spin systems or all spin systems (spin_system_#=0) in TOCSY, combined TOCSY and COSY, or combined TOCSY, COSY, and 1H-13C-HSQC spectra, using simulated annealing. This command can be used only within the Assign module, since it needs entities built by the Assign setup -- project entity, prototype pattern entity, residue list and all the used experiments with their peaks picked.
You must supply the numbers of the experiments from the project entity. The resulting spin systems are stored in the prototype pattern entity.
This search should begin with the longest spin systems. As the algorithm tries to fit peaks into a defined motif, it will not take care of possible additional correlated frequencies, which means that an AMX portion of a long spin system could be assigned to a four-spin system. Initially, the program should be run on the whole residue set of the primary sequence (which will automatically take into account the above-mentioned priorities) and on the patterns examined with the usual interactive tools, then rerun on specific missing amino-acid types. To compensate for the limited number of iterations in the simulated annealing, the process should be run for several loops (typically 6), from among which the program will retain the best results. One loop of the program for the whole sequence of a 53 residue protein requires about ten minutes of computation time on an R4000 Silicon Graphics Indigo workstation. For aromatic residues, this method assigns only the AMX subsystems, therefore the aromatic resonances should be found with the systematic search method and added through the clipboard.
This command can be run on any set of homonuclear or heteronuclear patterns (spin systems). It uses only the type and neighbors scores, obtained by any method, to find the sequence-specific assignment via simulated annealing optimization. Optionally, previous assignments are loaded and respected. The amino-acid type and/or residue number are considered assigned for a pattern if they are consistent over all frequencies of the pattern (unique or specified assignments).
After careful inspection of the patterns and scoring of types and neighbors, the process might be run on the full sequence. Then you might inspect the result, modify it, perhaps try another run, and identify some satisfactory parts from the scores listed. You should then discard the ambiguous assignments and rerun the program with the correct residues used as anchor points. If several such iterative processes still fail to determine unambiguously the complete assignment, then some additional information should be input, like a more accurate scoring or some new patterns.
The results are stored in assignment pointers for all frequencies of the patterns (and set as the current specified frequencies). Note that there should not be any residue named "null" in the molecule, else its assignment will be discarded.
Optionally, some parameters of the simulated annealing might be adjusted (scaled by a factor of 0.1 to 10) according to the complexity of the problem:
temp_factor, iter_factor: if most parts of the sequence are well defined these parameters can be decreased to speed up the program.
seq_factor: weight is accorded to the neighbors information, relative to the spin system fit scores.
The xyl command makes a database list of atom item numbers or frequencies based on specific selection criteria. The subcommands dealing with frequencies or patterns can be only used in conjunction with the Assign module (xyl frequency, xyl pattern, xyl shift, xyl multiple, xyl fp)
See also:
xyz Atom manipulation
atom defining center of a neighborhood (this may be an atom name, an item number, or -1 to select using the cursor) |
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xyl neighbors builds a list of atoms within a specified distance of a single atom. The list may be filtered based on a match with the string other, which may contain a wild card (*). The number of selected atoms is deposited in symbol.
xyl name builds a list of atoms matching the string atoms, which may contain a wild card (*). The number of atoms selected is deposited in symbol.
atom defining center of a neighborhood (this may be an atom name, an item number, or -1 to select using the cursor) |
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xyl atom builds a list of atoms within a specified distance of a single atom. The list may be filtered based on a match with the string other, which may contain a wild card (*). Also you can specify type, whether any atoms matching the above two criteria are to be collected to this list, or you need only assigned or only unassigned atoms. The number of selected atoms is deposited in symbol.
xyl frequency builds a list of assigned frequencies from the Assign database whose assignments match exactly the string atom, which may contain a wild card (*) for pseudoatoms. The number of frequencies selected is deposited in symbol.
xyl pattern builds a list of assigned patterns from the Assign database, whose assignments match the string atom, which may contain a wild card (*). The number of patterns selected is deposited in symbol.
xyl shift builds a list of singly assigned frequencies from the Assign database, within a range delta from a specified center. You have to specify whether the generic shifts or spectrum-specific shifts of the frequencies are to be compared with the target shift. The number of selected frequencies is deposited in symbol.
xyl multiply builds a list of multiply-assigned frequencies from the Assign database within a range delta from a specified center. You have to specify whether the generic shifts or spectrum-specific shifts of the frequencies are to be compared with the target shift. The number of selected frequencies is deposited in symbol.
xyl fp builds a list of patterns from the Assign database which contains the target frequency. The number of patterns selected (usually one) is deposited in symbol.
In addition to real and complex data, Felix supports yet another data type, namely (x,y) pairs of data. Each data point is actually stored as a triplet and consists of an abscissa (x), an ordinate (y), and a sigma or error term for y.
These lists of (x,y) pairs can be displayed using the dr command, saved and retrieved from buffers, edited to add and delete points, written to and read from files, and fitted to a variety of functions to yield model parameters. The reserved symbol linpts specifies the style in which the data is displayed:
Symbol dependence:
linpts Display style
Symbols changed:
datype data type
datsiz number of datapoints
disply current display type
stack stack depth
See also:
dr draw workspace
lvo load volume time course
xyp zero zeroes the workspace, and changes the data type to (x,y) pairs.
xyp add adds a single data point to the work space.
xyp delete deletes a single data point from the work space.
xyp cursor add adds a single point to the workspace. This operation requires a current plot to establish graphics context. A crosshair cursor is enabled, allowing you to select an (x,y) location and click the mouse button to add the point. The new sigma_y is set to one.
xyp cursor delete allows you to use the cursor to select a point to be deleted from the workspace. A crosshair is enabled, which may be used to delete a point by placing it over the point and clicking the mouse button.
xyp get loads the values from a specified point number pt# into the symbols symbol_x, symbol_y and symbol_sigma.
xyp label specifies the label units for the x and y axis to be annotated on plots.
xyp sort sorts the (x,y) points based on x value, y value, or sigma value. To draw the data with lines connecting the points, the data must be sorted by x value in ascending order.
xyp read reads in an ASCII file containing (x,y) pairs into the work space. The format of the file is:
Line 1: label text for both axes (2a20)
Line 2-N: X_value Y_value sigma_value (space delimited)
xyp write writes the (x,y) pairs in the work space to an ASCII file with format as specified above.
polynomial (order is next parameter) f(x)=A0+A1*x+A2*x*x+A3*x*x*x... |
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simple exponential with explicit zero intercept f(x)=A0*exp(A1*x) |
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xyp fit performs a least-squares fit of the (x,y) data in the work space to the specified model function. The resulting coefficients are saved into the symbol coefN, where N is the coefficient number. The sigma value for each coefficient is saved into the symbol sigmN, corresponding to each coefficient. The error of the fit is returned in the chisq symbol. Following the fit, buffer 1 contains the model data and stack is set to one. Subsequent draws using dr plot both the original and model data.
polynomial (order is next parameter) f(x)=A0+A1*x+A2*x*x+A3*x*x*x... |
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simple exponential with explicit zero intercept f(x)=A0*exp(A1*x) |
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xyp build performs a curve calculation using the symbols coefN, where N is the coefficient number. The function for the curve calculation is defined by the parameter function and the command will expect the coefficients to be in right symbol. The reconstruction will happen only if the workspace is in (x,y) pair form. The reconstructed curve is stored in buffer 1 and by subsequent drawing command the theoretical curve is getting drawn on the current x,y plot.
The xyz command provides a number of operators that act on atomic coordinates. These operators allow you to display, identify, label and interact with structures graphically while maintaining a connection to all NMR-related information.
Symbols changed:
disply current display type
See also:
bck back calculation
xyl atom list manipulation
xyz draw displays the current molecule. The atoms are drawn using their current attributes, which include color, visibility and label. These attributes may be changed using other xyz operators.
xyz who enables a crosshair cursor and allows you to select an atom, then returns the item number of the atom in symbol. If no atom is selected, symbol is set to zero (0). This operator works both on "flat" and 3D displays.
filetype: 0=PDB format, 1=Insight II format, 2=X-PLOR PDB format and the names stored as Insight II names (used in Assign) 3=MDL MOL format (used in Analytical) |
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xyz read reads an ASCII file containing atomic coordinates. This operator builds DBA entities for atoms, attributes and residues. For PDB files, the file name can have an explicit extension (the default is .pdb). Insight II files should not include an extension, as the command will look for both file.mdf and file.car.
If type=2 the X-PLOR type PDB file can be read in and the names of the atoms stored in Insight II type notation: 1:residuename_residuenumber:atomnamenumber
If type=3 the MDL MOL file can be read in.
atoms(s) to label (by item#, DBA, match string, or -1 for cursor) |
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redraw status: 0=no redraw, 1=redraw now to show label change |
xyz label labels one or more atoms in the current display with corresponding full atom names. Labels may be turned on and off. The atom(s) may be selected by item number, crosshair cursor, or by giving a DBA list specifier (1#) or a match string. A match string may include a wild card character (*). The display can be automatically redrawn following the label change, or you can issue a number of xyz label operations before redrawing the display.
atoms(s) to label (by item#, list, match string, or -1 for cursor) |
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redraw status: 0=no redraw, 1=redraw now to show label change |
xyz visible makes atoms visible or invisible. The atom(s) may be selected by item number, crosshair cursor, or by giving a DBA list specifier (1#) or a match string. A match string may include a wild card character (*). The display can be automatically redrawn following the visibility change, or you can issue a number of xyz visible operations before redrawing the display.
atoms(s) to label (by item#, DBA, match string, or -1 for cursor) |
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redraw status:0=no redraw, 1=redraw now to show label change |
xyz color sets the display color of the specified atoms. The atom(s) may be selected by item number, crosshair cursor, or by giving a DBA list specifier (1#) or a match string. A match string may include a wild card character (*). The display can be automatically redrawn following the visibility change, or you can issue a number of xyz color operations before redrawing the display.
xyz distance calculates the distance between two specified atoms. Each atom may be selected by item number, DBA list, crosshair cursor, or by atom name. If both atoms exist, the interatomic distance in angstroms is returned in symbol. If any of the atoms is a pseudoatom, the effective distance is calculated.
Any error returns a distance of zero.
xyz pattern draws a line of the specified color connecting two atoms. Each atom may be selected by item number, DBA list, crosshair cursor, or by atom name. This operator is commonly used to graphically display interactions between spin pairs (e.g., distance monitors).
xyz clear deletes all the entities connected to the molecule (xyz:atoms, xyz:bonds, xyz:residues, and xyz:atm_atr).
The xyz current command makes the entities connected to the molecule current. This command acts as if an xyz read command were executed, therefore this is an alternative to that command, if the molecule was read into a database during a previous session and saved. Use this command to let Felix know that there is a valid molecule in the memory.
xyz assembly reads an ASCII file containing an ensemble of molecules in Insight II sequential archive format (.arcs). The specification should not include an extension, as the command will look for both file.mdf and file.arcs.
ze causes the data in the workspace to be set to 0.0.
Symbol dependence:
datsiz number of datapoints
See also:
set set workspace to value
zf expands the data in the work space to a larger size, filling the additional space with zeros. The zero fill command is used before Fourier transformation to improve digital resolution. The default new size is the next integral power of two that is larger than the current size.
Symbol dependence:
datsiz number of datapoints
Symbols changed:
datsiz number of datapoints
zgt zeroes all points in the work space that are greater than the specified threshold value. This is a brutal way to wipe out big peaks in your spectrum. The zgt command is sometimes used to remove a water peak from a spectrum in order to speed up the plotting process.
Symbol dependence:
datsiz number of datapoints
datype data type
zi zeroes the imaginary part of the data in the workspace.
Symbol dependence:
datsiz number of datapoints
datype data type
zlt zeroes all points in the work space that are less than the specified threshold. This is a drastic way to wipe out baseline noise, as well as small peaks.
Symbol dependence:
datsiz number of datapoints
See also:
zgt zero greater than
zr zeroes the real part of the data in the workspace.
Symbol dependence:
datsiz number of datapoints
datype data type
This command is similar to np, except that it does not draw the axis and labels.