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.
flf - FaceLift baseline correction
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.
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
csp - Cubic spline baseline correction
flf - FaceLift baseline correction
pol - Polynomial baseline correction
bas - Baseline points manipulation
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.
ldb - Load buffer into work space
stb - Store work space to buffer
mul - Multiply the 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.
log - Natural logarithm of work space
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.
sep - Separate real and 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, define the symbol pltann to 1 before issuing the hcp command.
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.
phase0 Zero order phase correction
phase1 First order phase correction
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 below:
abq - Automatic selection of baseline points
csp - Cubic spline baseline correction
flf - FaceLift baseline correction
pol - Polynomial baseline correction
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:
bck spectrum_id bckxpk bckvol mix rleak
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 Chapter 2, "Theory", in the FELIX User Guide. bck will efficiently generate expected spectra, and is very useful when generating structures from NOE data.
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.
ift - Inverse Fourier transform
This set of commands allows you to read the NMR Refine database files from the disk.
rreent Current resonance table
ins - Insight II-FELIX inter-process communication
biw - Write database to Insight II
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 to the NMR Refine database files to the disk.
In the following example, a three-dimensional matrix called test.mat, 512 ¥ 256 ¥ 32 points, is created.
bld test 3 512 256 32
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.
ins - Insight II-FELIX inter-process communication
bir - Read database from Insight II
biw - Write database to Insight II
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.
vector Number of Vectors in the Entire Bundle
lwb - Load work space from bundle
swb - Store work space 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.
exr - Execute a macro and return
rf - Read FELIX for Windows file
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.
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.
frsize Workspace and Buffer Size
cgd updates symbols on a non-modal (mnu a) control panel.
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.
wr - Write a file (old format)
wn - Write a file (new format)
clr causes the current graphics frame to be erased. The frame will no longer have any current graphics context or mapping.
cls closes the current output file. Unless an output file is open, the put record command (put) will take no action.
cmx closes all open matrix files. The matrix buffer is also de-allocated.
dimen Number of Matrix Dimensions
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.
lpx - General linear prediction
lpf - Linear predict first points
lpl - 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.
animat Specifies Video-Buffering
clmode Selects Linear or Geometric Contour Spacing
erase Disables(0)/Enables(1) Automatic Screen Erasing
grid Specifies Superimposed Grid Lines
nlevel Number of Contour Levels
posneg Enables Plotting of Negative Contour Levels
projct Selects Dimensionality of Display
rowinc Point Skipping Factor for 3D Displays
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.
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. Accelrys recommends using pol for baseline correction during transforms.
abq - Automatic selection of baseline points
flf - FaceLift baseline correction
pol - Polynomial baseline correction
bas - Baseline points manipulation
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:
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 6., Database and tables, contains detailed information on all aspects of its use.
dbl doubles the size of the data in the workspace by performing a linear interpolation between the existing data points.
def count 10
In this example, the symbol count is given an explicit number value of 10. Subsequently, if you run a macro containing the following command:
for rows 1 &count
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: 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.
Only the symbol named in the def command
eva - Evaluate expression and assign to symbol
der takes the derivative of the data in the workspace and pushes it onto the current buffer stack. The workspace is left unchanged.
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
Accelrys/Felix 2002/macros/mac
directory and should be called according to the version number:
bphase.dspfvs
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.
decim Decimation factor (from BRUKER DECIM variable in acqus)
dspfvs Oversampling version (from BRUKER DSPFVS variable in acqus)
bft - Bruker-Fourier transform
ift - Inverse Fourier transform
dir get returns the current working directory to symbol curdir. If
curdir is omitted, it displays the current working directory on the status bar.
dir set sets the current working directory as a curdir (a valid folder name expected, otherwise it is ignored). Once the current working directory has been changed, any paths relative to ".\" is changed.
dr draws the contents of the workspace (default) as well as the number of buffers indicated by the stack depth symbol stack.
animat Enable Double Buffering
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.
drx &pksent 4 (using entity name)
drx L2 6 (using DBA list number)
drx pksent -4 matfil color (Overlays pksent referenced by matfil on current matrix using color color)
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.
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:
repek1 = 1
repek2 = 3
repek3 = 2
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:
dst compname number_of_processors first_bundle number_of_ bundles tmp_dirNote 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:
exd macro arg1 ... argNThis 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:
donThe 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:
dofExecuting 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.
- The original process should not alter the matrix until the distributed processing is done. Thus, the macro should be carefully written not to start for example, a second dimension processing, until the first is finished.
- The temporary directories should be accessible from the computer where the original FELIX runs (for example, ls should work).
- As with all distributed programs, higher processing/disk I/O ratio equals better efficiency; do not use this command for only Fourier transforming a small data set, but rather use it for a big 3D or 4D processing with LP.
- This processing can be used only after the data in the FELIX matrix format; that is, generally it is not applicable to the first dimension processing, unless it is imported into a FELIX matrix format before starting the transformation.
eif - Macro end of block ifeif defines the end of a block-form macro if statement. See the if documentation for a complete description of the if/else syntax.
els - Macro else blockels 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 - Exponential multiplyem line broadening
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. The swidth parameter must be set correctly; otherwise, the window function will be improper.Symbol dependence:
ena - Enable multiple cursorsena frame on/off
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.See also
end - Macro end statementend terminates macro execution and returns to command mode. end is only valid in macros.
env - Get a system environment variableenv env_var symbol
env allows the user to read the system 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 - Macro branch on error conditionerr label macro_label
err macro macro_file_name
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.
esc - Test for escape key eventesc symbol
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.CautionBe 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 - Evaluate expression and assign to symboleva symbol_name expression num_of_characters
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:eva count (&row*5)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.
See also
ex - Execute a macroex macro arg1 ... argN
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 for more information.
Symbol changedSee alsoexr - Execute a macro and return
go - Macro unconditional branch
exc - Exchange real and imaginaryexc
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
exm - Execute Multiple Macrosexm macro arg1 ... argN
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 for more information.
See alsoexr - Execute a macro and return
exp - Expanded displayexp
exp generates an expanded display of the workspace using the current 1D plot limits (first, last).
Symbol dependenceSee alsodr - Draw work space and stack
exr - Execute a macro and returnexr macro arg1 ... argN
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" in Chapter 4., Macros for more information.
See also
fit - Fit 1D peaksfit
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.
fit peak_entity volume_entity slot_number optimize_center optimize_widths optimize_heights
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:See alsossp - Synthesize spectrum from peak list
flf - FaceLift baseline correctionflf baseline filter_width num_std_dev smooth_pnts buff_no
flf correct filter_width num_std_dev smooth_pnts
flf smooth filter_width buff_no
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
fli - Frequency list manipulationThe 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.
fli clear list
The clear subcommand removes all values from the specified frequency list.
fli add list freq freq ...
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.
fli list list
The list subcommand lists (on the screen) the chemical shift values stored in the specified frequency list.
fli delete list lo_freq hi_freq
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.
fli union list1 list2 list3
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.
fli draw D1list D1color D2list D2color obj#
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 0 then it erases the displayed frequencies. If the D1color or D2color is -1 then each frequency in the list will have a different color.
fli object D1list D1color D2list D2color obj#
See draw (dr - Draw work space and stack).
fli tile D1list D2list tile_width tile_entity
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.
Symbol dependenceThe fli draw D1list D1color D2list D2color obj# command affects the following user symbols:
flid1 Current frequency list number on D1, set to the value of D1list.
flid2 Current frequency list number on D2, set to the value of D2list.
flicol1 Color to display frequencies on D1, set to D1color.
flicol2 Color to display frequencies on D2, set to D2color.
See alsofli read list freq_entity
The read subcommand copies the chemical shift values in the database frequency list entity freq_entity to the specified frequency list.
fli write list freq_entity
The write subcommand copies the chemical shift values in the specified frequency list to the database frequency entity freq_entity.
fli move list1 list2
The move subcommand copies the chemical shift values in list1 to list2.
fli equiv list resolution
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.
fli xpks list peaks dimen 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.
fli peak list peaks resolution
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.
fli an list freq name
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.
fli rc list clipboard_entity
The rc subcommand copies the chemical shift values and names in the assign database frequency clipboard entity clipboard_entity to the specified frequency list.
fli rn list pattern_entity pattern_# spectrum_id
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).
fli rp list protopattern_entity proto_#
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_#).
fli collect list pattern_entity spectrum_id centrum delta
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.
fli sort list order
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 - Low-point fold of work spaceflp
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 dependenceSymbol changedSee also
flt - FLATT baseline flatteningflt baseline_width chimin number_of_points tau
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 dependenceSee alsochi - Calculate minimum chi-square value
flf - FaceLift baseline correction
fol - Fold work space in halffol
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 dependenceSymbol changedSee alsoflp - Low-point fold of work space
for - Loop for macrosfor symbol start end step
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.
fpo - Pop FELIX windowfpo
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.
fpu - Push FELIX windowfpu
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 - Manipulate graphics framesfra op parameters
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 X_origin Y_origin X_size Y_size
fra open -1
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
fra zero closes all frames and re-initializes the frame manager.
fra front frame#
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
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 X_origin Y_origin
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 X_origin Y_origin X_size Y_size
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 frame# symbol
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 frame# header text
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 symbol symbol2 symbol3
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. The optional symbol symbol2 amd symbol3, if present, receive the count of opened frames and the maximum ID of them.
fra 3D_reset
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
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
fra unexpand restores an expanded frame to its previous size and location. The current plot is automatically redrawn.
fra j
fra j iconifies the current frame. The current plot is automatically redrawn.
fra k
fra k restores an iconified frame to its previous size and location. The current plot is automatically redrawn.
fra n x0 y0 x1 y1
fra n returns the current coordinates of the active frame.
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 frame#
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 frame#
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 frame# mode symbol_name local_symbol
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
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 frame#
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.
fra link frame_n dimension_a frame_m dimension_b
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.
fra y frame_n dimension_a frame_m dimension_b
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.
fra y
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.
fra 0
Temporarily disables frame connection
fra 1
Restores frame connection if it was defined before.
ft - Fast Fourier transformft
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 dependenceSee alsodft - Fast Fourier transform of digitally oversampled data
bft - Bruker-Fourier transform
ift - Inverse Fourier transform
ful - Full displayful
ful draws the entire 1D spectrum in the current frame. ful is the opposite of the exp command.
Symbol changedSee also
fxp - Filter cross peaksfxp peaks diagonal tolerance confirm
fxp peaks doublets tolerance
fxp peaks asymmetric tolerance confirm
fxp peaks width min_width max_width confirm
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 dependencehafwid Cross Peak Half Width Factor
See alsofxp peaks diagonal tolerance
fxp confirm (units type)
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.
fxp peaks doublets tolerance
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.fxp peaks asymmetric tolerance confirm (units type)
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.fxp peaks width min_width max_width confirm
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 - Get a symbol valueget prompt_string symbol_name
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
gf - Generate FIDgf amplitude frequency tau
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 dependenceSee also
gif - Macro arithmetic gotogif expression label1 label2 label3
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 - Gaussian/Lorentzian windowgm broadening coefficient
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:
gmh - Gaussian multiply in Hzgmh broadening
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 - Macro unconditional branchgo macro label
go is used within macros to perform an unconditional branch to the specified label.
gre - Greek text annotationgre x0 y0 (z0 a0) (fix) (anchor) number text
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:A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
A B C D E F G H I J K L M N O P Q R S T U V W X Y Za b c d e f g h i j k l m n o p q r s t u v w x y z
a b c d e f g h i j k l m n o p q r s t u v w x y zSymbol dependenceSee also
gto - Macro case gotogto expression label0 label1 ... labeln
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 - Generate spectrumgsp intensity frequency Lorentzian Gaussian
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 - Get valuegv point real symbol_name imaginary symbol_name
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 dependenceSee also
hav - Halve data sizehav
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 dependenceSymbol changedSee also
hcp - Hard copy plothcp
hcp preview
hcp setup
The printing of FELIX is WYSIWYG, so the parameters that affects spectral display on the screen also affects the printout. The parameters used in the previous versions that only controlled hardcopy, such as hardmo, harddv, papwid, paphgt, hardx0, hardy0, hardxs, hardys, pltorg, and orient, are all obsolete.
hcp setup displays the standard Print Setup dialog for you to select printers, set page properties, etc.
hcp preview displays the standard Print Preview.
hcp displays the standard Print dialog box and submit the print job if you click OK.
Note: Depending on which frame is the active, hcp applies to both spectral display and spreadsheet display.
See alsodr - Draw work space and stack
sca - Scale factor for dimension
hft - Hilbert transformhft mode
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 dependenceSee alsobft - Bruker-Fourier transform
ift - Inverse Fourier transform
idf - Is definedidf test_symbol ans_symbol
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
if - Macro if conditional branchif expression1 operator expression2 macro_label
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:
Advanced if conditionals1. 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 expression op expression and expression op expression ...
if expression op expression or expression op expression ...
Macro if conditional block executionThe 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.
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 - Inverse Fourier transformift
ift performs an inverse Fourier transform; it transforms a complex frequency-domain spectrum into a complex time-domain FID.
Symbol dependenceSee alsodft - Fast Fourier transform of digitally oversampled data
bft - Bruker-Fourier transform
inq - Inquire If file existsinq ext file_name symbol
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 changedThe symbol specified as a parameter is set to zero or one.
ins - Insight II-FELIX inter-process communicationins keyword rest_of_command_line
ins initialize
The ins initialize command initializes the FELIX server.
ins connect
The ins connect command connects FELIX to Insight II.
ins check
The ins check command checks to see if the RPC connection is currently up
ins command rest_of_command_for_Insight
ins command passes the command string to Insight II, substituting the atom specification from the NMR spec into an Insight II spec.
ins command2
ins command2 passes the string to Insight II as is, without converting the data format.
ins getdir
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 - Integralint
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 changedSee also
inv - Inverse of workspaceinv
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 - Intensity plotip
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 dependenceanimat Specify Video-Buffering
clmode Selects Linear or Geometric Contour Spacing
nlevel Number of Contour Levels
posneg Enables Plotting of Negative Contour Levels
projct Select Dimensionality of Display
rowinc Point Skipping Factor For 3D Displays
Symbol changedSee also
jcp - Calculate J-coupling constantjcp peaks item who j1val j2val j1sig j2sig
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 dependenceoptmth optimization method for DQF-COSY or E-COSY J coupling extraction: Quasi-Newton (0), simplex (1) or simulated annealing (2).
kw - Kaiser windowkw size parameter
kw is a window function described in Hamming's book Digital Filters. This window is useful for apodizing truncated data.
ld - List datald first last
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.See also
ldb - Load buffer into work spaceldb buffer
ldb loads the contents of the specified buffer into the work space.Symbol dependenceSee alsoswb - Store work space to bundle
lim - Matrix limitslim dimension first_point last_point
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 changedlolimn Low Limit For Dimension N
hilimn High Limit For Dimension N
See also
lin - Line annotationlin x0 y0 (z0 a0) x1 y1 (z1 a1)
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 dependenceSee also
lis - List symbol tablelis optional_specifier
lis displays current symbols and their values. The optional specifier may contain a * wildcard to list only specified symbols.
See also
lm - List macrolm file_name
lm lists the current or specified macro.
loa - Load vector from matrixloa dim1 dim2 dim3 ...
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 changeddnvect Vector Coordinates Along Dimension N
See alsolwb - Load work space from bundle
log - Natural logarithm of work spacelog
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 dependenceSee alsoaln - Antilogarithm (exponential) of work
lmd - Load theoretical vectorlmd dim1 dim2 dim3 ...
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 changeddnvect Vector Coordinates Along Dimension N
See also
lpf - Linear predict first pointslpf points coefficients peaks first
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:See alsolpl - Linear predict last points
lpl - Linear predict last pointslpl points coefficients peaks first last reflect
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 dependenceSee alsolpf - Linear predict first points
lps - Solvent suppression using linear predictionlps points peaks threshold
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
lpx - General linear predictionlpx use_first use_last predict_first predict_last coefficients method reflect mode
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 dependenceSee alsolpl - Linear predict last points
lpf - Linear predict first points
lrl - Find local extremumThe lrl commands finds local minimum, maximum or extremum in the current spectrum.
lrl max lopt1 hipt1 ... loptn hiptn symbol_posN symbol_int
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:
lrl max -1 symbol_posN symbol_int
If (lopt1) is set to 0 it finds the maximum intensity position within the current plot limits:
lrl max 0 symbol_posN symbol_int
lrl min lopt1 hipt1 ... loptn hiptn symbol_posN symbol_int
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:
lrl min -1 symbol_posN symbol_int
If (lopt1) is set to 0 then it finds the minimum intensity position within the current plot limits:
lrl min 0 symbol_posN symbol_int
lrl ext lopt1 hipt1 ... loptn hiptn symbol_posN symbol_int
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 ext -1 symbol_posN symbol_int
If (lopt1) is set to 0 it finds the local extremum intensity position within the current plot limits:
lrl ext 0 symbol_posN symbol_int
lrl pma loppm1 hippm1 ... loppmn hippmn symbol_posN symbol_int
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 loppm1 hippm1 ... loppmn hippmn symbol_posN 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 loppm1 hippm1 ... loppmn hippmn symbol_posN 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 - Load volume time courselvo volumes item# (start)
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 changedSee alsovol - Integrate cross peak volumes
xyp - X,Y data pair manipulation
lwb - Load work space from bundlelwb
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 changedSee alsoswb - Store work space to bundle
mat - Open matrixmat file_name access storage
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 dependenceSymbol changeddimen Dimensionality of Matrix
See also
md - Model datamd real model peaks volumes slot
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.md 1 0 (Display real data only - disables model data)
md 0 1 peaks volumes 1 (Display model data only)
md 1 -1 peaks volumes 1 (Display difference (real minus model)
mf - Matched filtermf rho lbroad
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:Symbol changed:
mgv - Matrix get data value
mpv-Matrix put data valuemgv dim1 dim2 dim3 ... symbol
mpv dim1 dim2 dim3 ... value
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
mmp - Display memory mapmmp
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.
See also
mnu - Menu managermnu op parameters
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 panelsmnu bar motfile X_origin Y_origin
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.
mnu gauge 1 max_value text_message
mnu gauge 2 cur_value
mnu gauge 3
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.
Table 3: defines a new meter gauge, gives the uppermost value, puts the meter on the center of the FELIX display, and labels it with the text message
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.
mnu remove menufile
mnu remove all
Remove one menu from the display, or remove all menus if all is specified.
mnu p menufile X_origin Y_origin
Draws an interactive control panel (dialog box) 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 Chapter 5., Menus and control panels for a description of the content of control panel files.
mnu a menufile X_origin Y_origin
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 button (unless you explicitly hold the macro flow using wai). ). See Chapter 5., Menus and control panels for a description of the content of control panel files.
mnu h option (text)
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.
Symbol changed
ms - Magnitude spectrumms
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.
See also
mul - Multiply the work space by a numbermul real_multiplier imaginary_multiplier
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 dependenceSee also
mwb - Multiply work by buffermwb buffer
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 alsostb - Store work space to buffer
ldb - Load buffer into work space
nd2 - Neighbor detection in 2D NOESY spectrumThis 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.
nd2 tol tolerance
This command string defines the frequency collapse tolerance, to judge whether a candidate frequency is a new one.nd2 noe noecon noepks
nd2 pat loppm hippm maxfrq
nd2 lev outlev
nd2 norm false/true
This command utilizes the normalize option, which normalizes the scores for each pattern to one.
nd2 ran loppm hippm
nd2 nei number
nd2 rto tolerance
nd2 exe nosypk */patnum
nd3 - Neighbor detection in 3D NOESY spectrumThis 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.
nd3 met method
This command string defines the method for neighbor detection - namely using homonuclear or heteronuclear spectrum.nd3 tol tolerance
This command string defines the frequency collapse tolerance, to judge whether a candidate frequency is a new one.nd3 noe noecon noepks
nd3 pat loppm hippm maxfrq
nd3 lev outlev
nd3 norm false/true
This command utilizes the normalize option, which normalizes the scores for each pattern to one.
nd3 ran loppm hippm
nd3 sto number
nd3 rto tolerance
nd3 seq loppm hippm
This command string defines the frequency range for the 15N resonances in the pattern s in the case of heteronuclear neighbor detection.nd3 rev t/f
This command string defines whether the program should look for reverse NOE contacts appearing in, e.g., 3D TOCSY-NOE spectra.nd3 shi loppm hippm
nd3 nsc score
This command string defines the neighbor score option (values between 0 and 3), used when the reverse NOE-contact option is on.nd3 nuc nucleus1 nucleus2
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 throughnd3 ran 5.5 12.0command for a protein and. The nucleus2 should be set to N and the range should be defined through
nd3 seq 90.0 130.0If a homonuclear spectrum is being used for neighbor detection, both nucleus1 and nucleus2 should be set to H.
nd3 cdm dimension
nd3 stm method
nd3 exe nosypk */patnum
nex - End of a loopnex
nex defines the end for a for loop in macros. This command is only valid in macros.
See also
no - Generate random noiseno amplitude
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
nop - No operationnop
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 - Normalize datanor data point new value
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 - Null plotnp
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
old - Recall old limitsold
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
opn - Open output fileopn extension file_name access_mode
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 alsorea - Read record from ASCII file
opt - FELIX option license inquiry or license checkin and checkoutopt number symbol
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 Accelrys (see the FELIX Getting Started document).
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 - Matrix dimension orderord dim1 dim2 ... dimN
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.See also
ovc - Overlay contour plotovc (options)
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
ovc clear
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.
ovc set spectrum_id
The set option specifies which spectrum from the database should be overlaid. You have to call this command at least two times.
ovc connect spectrum_id dimension spectrum_id dimension
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.
ovc
Finally, calling the ovc command, with no options, draws the overlay plot.
pd2 - Prototype pattern detection in 2DAfter 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.
pd2 seed d1high d1low d2high d2low
This command is useful only for macromolecules.
pd2 exp d1high d1low d2high d2low
This command is useful only for macromolecules.
pd2 tol tol tol2
pd2 res rppmin rppmax lopmax resmax
This command is useful only for macromolecules.
pd2 rem logical
pd2 lev outlev
This command is useful only for macromolecules.
pd2 con cos contact2 contact3 contact4 contact5
pd2 con cot contact2 contact3 contact4 contact5
pd2 con ctn contact2 contact3 contact4 contact5
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.
pd2 nfi fltnum
This command is useful only for macromolecules.
pd2 fil number loppm# hippm# min# max#
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
pd2 ent cos cosy peak entity
pd2 met cos
These command strings specify the COSY peak entity, and define the method to be based on COSY spectrum.
pd2 ent toc tocsy peak entity
pd2 met toc
These command strings specify the TOCSY peak entity, and define the method to be based on TOCSY spectrum.
pd2 ent toc tocsy peak entity
pd2 ent noe noesy peak entity
pd2 met tno
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.
pd2 ent toc tocsy peak entity
pd2 ent cos cosy peak entity
pd2 ent noe noesy peak entity
pd2 met ctn
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.
pd2 ent hmq hmqc peak entity
pd2 ent cos cosy peak entity
pd2 met qco
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.
pd2 ent hmq hmqc peak entity
pd2 ent toc tocsy peak entity
pd2 met qto
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.
pd2 ent hmq hmqc peak entity
pd2 ent cos cosy peak entity
pd2 ent toc tocsy peak entity
pd2 met qct
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.
pd2 ent hmq hmqc peak entity
pd2 ent cos cosy peak entity
pd2 ent hmb hmbc peak entity
pd2 met qcb
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.
pd2 ent hmq hmqc peak entity
pd2 ent toc tocsy peak entity
pd2 ent hmb hmbc peak entity
pd2 met qtb
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.
pd2 exe
This command string executes the pd2 command for macromolecules.
pd2 ana
This command string executes the pd2 command for small molecules.
Symbol dependencerprent Prototype pattern entity
pd3 - Prototype pattern detection in 3Dpd3 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:
pd3 seed d1low d1high d2low d2high d3low d3high
pd3 exp d1low d1high d2low d2high d3low d3high
pd3 tol tol
pd3 res rppmin rppmax lopmax resmax
pd3 rem logical
pd3 lev outlev
pd3 jco contact2 contact3 contact4 contact5
pd3 jno contact2 contact3 contact4 contact5
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.
pd3 nfi fltnum
pd3 fil number loppm# hippm# min# max#
pd3 use used1 used2 used3
For heteronuclear detection you usually need to use the HN and N frequencies of the seed peaks.pd3 uex used1 used2 used3
For heteronuclear detection you usually need to use the aliphatic H frequencies of the expansion peaks.pd3 rot dimension
pd3 met method
This command string specifies the method to base on the prototype pattern detection.pd3 exe peaktable (seed_peaks)
This command string executes the pd3 command.Symbol dependencerprent Prototype pattern entity
pen - Define a new colored penpen pennum R G B color_table_size
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.
pen read pennum ired igreen iblue
This returns the rgb values for the pen number in the ired, igreen, and iblue symbols
ph - Phase correctionph
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 dependencephase1 First-order phase angle
See also
pic - Peak pick and labelpic
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.
For 1D spectrapic entity pick_mode symbol
pic picks 1D peaks and stores them in the database entity.
0=build new entity of all peaks in current display
1=append to existing entity all peaks in current display
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 dependenceposneg Positive/negative peak switch
Symbols changedpicent Current peak pick entity
For ND Spectrapic peak_style entity pick_mode symbol
pic peak_style entity pick_mode symmetry symbol
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:
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:
0=build new entity of all peaks in the display
1=append to existing entity all picked peaks in the display
2=append to existing entity a single peak with the cursor*
3=append to existing entity multiple peaks selected using a rubber band cursor*1
4=append to existing entity a single peak at the location defined by the point (x0pnt, y0pnt)
5=append to existing entity multiple peaks in the box defined by the two points (x0pnt, y0pnt) and (x1pnt, y1pnt)
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 dependencehfwid1 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
Symbols changedpksent Current cross peak entity
piv - Set the pivot for phase correctionpiv flag
piv displays (if flag = 1) a small red triangle under the 1D axis that shows the pivot point for real-time phase correction. If flag = 0, it hides the pivot.
Symbol dependencepivot The data point used as a pivot for phsae correction.
See also
pla - Redisplay 3D objectpla
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 - Polynomial baseline correctionpol order
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 dependenceSee alsoabl - Automatic baseline flattening
abq - Automatic selection of baseline points
bas - Baseline points manipulation
csp - Cubic spline baseline correction
flt - FLATT baseline flattening
pop - Pop the display stackpop
pop causes the buffer stack head to be moved to the workspace and decreases the value of the stack depth parameter (stack).
Symbol dependenceSymbols changedSee alsoldb - Load buffer into work space
psh - Push the work space onto the buffer stack
stb - Store work space to buffer
xsh - Exchange stack head with work space
ppm - Convert Between points and PPMppm dim mode value symbol
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.
prb - Residue type probability scoringprb Cappm Cbppm (pattern#)
This command uses the Grzesiek-Bax method (Grzesiek and Bax 1993) to calculate residue type probabilities from the C and C 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 output window.
prf - Formatted printprf format symbol1 ... symboln result
prf puts a format description (FORTRAN style) for printing variables (symbols) into a string (symbol). For example:prf `i1,1x,a5,1x,f7.3,1x, "This is the end"' &myint `&mytext' &myreal resultprints an integer, then text, then a real number, and then the quoted text to the variable (symbol) result.
The allowed format directives are:
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 - Power spectrumps
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.
psa - Suggest assignment for a set of patternsThis 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.
psa asn asspro neipro
psa lev outlev
psa sto logical
This command stores and sort assignments or prints them as they are determined.psa res firres lasres minlen maxnas
psa pri maxpas
psa rto rottol
psa exe stretch
This command string executes the psa command and stores the resulting stretches in the stretch entity.
psh - Push the work space onto the buffer stackpsh
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 dependencedatsiz Number of datapointsdatype Data typeSymbols changedSee also:
pso - Polynomial-based solvent suppressionpso window order
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 dependenceSee alsolps - Solvent suppression using linear prediction
puf - Formatted putpuf format symbol1 ... symboln
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:puf `i1,1x,a5,1x,f7.3,1x, "This is the end"' &myint `&mytext' &myrealprints an integer, then a text, then a real number, and then the quoted text to the previously opened file.
The allowed format directives are:
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.
pur - Purge symbol tablepur symbol_list
The pur command purges the symbol list, causing user-defined symbols to be deleted. The symbol can be wildcarded:pur abc*which purges all variables having the first three letters "abc".
put - Put recordput text
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
pv - Put valuepv point real_value imaginary_value
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.See also
pxp - Automated peak assignmentThis command can be used to automatically assign peaks after the spin systems are assigned to specific atoms.
pxp mul yesno (entity)
pxp lev outlev
pxp any enforce skipful skipmul
psa tau tauc cutoff specfrq t1leak unamb_dis
pxp exe entity
This command string executes the pxp peak autoassignment command using the entity peak table.
qsb - Skewed sinebell windowqsb size shift skew
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 dependenceSee alsoqss - Skewed sinebell squared window
qss - Skewed sinebell squared windowqss size shift skew
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 alsoqss - Skewed sinebell squared window
ra - Read ASCII datara file_name
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.See also
rb - Read Bruker filerb file (process_#)
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 dependenceSymbols changedphase1 First-order phase angle
See alsorf - Read FELIX for Windows file
re - Read a file (old format)re file_name
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 dependenceSymbols changedphase1 First-order phase angle
See alsorf - Read FELIX for Windows file
rea - Read record from ASCII filerea
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
rec - Rectangle annotationrec x0 y0 x1 y1
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 dependenceSee also
red - Reduce complex to realred
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 dependenceSymbols changedSee also
ref - Set shift referenceref point shift
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 dependenceSymbols changed
ret - Macro subroutine returnret
ret returns control from a called macro to the calling macro.
See alsoexr - Execute a macro and return
rev - Reverserev
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
rf - Read FELIX for Windows filerf file_name
rf reads an FID from the FELIX for Windows file_name into the 1D work space.Symbol dependenceSymbols changedphase1 First-order phase angle
See alsorf - Read FELIX for Windows file
rft - Real Fourier transformrft
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 dependenceSymbols changedSee alsoift - Inverse Fourier transform
bft - Bruker-Fourier transform
rj - Read JEOL filerj file_name
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 dependenceSymbols changedphase1 First-order phase angle
See alsorf - Read FELIX for Windows file
rm - Read macrorm file_name
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 dependenceSymbols changed
rmx - Reference matrixrmx dim freq width axis refpt refval text
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.
rmx -dim sym1 sym2 sym3 sym4 sym5 sym6
rn - Read file (new format)rn file_name
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 dependenceSymbols changedphase1 First-order phase angle
See alsorf - Read FELIX for Windows file
rph - Real-time phaserph
This command is obsolete in FELIX. It has been replaced by macros that use modeless control panels to realize real-time phasing. See macros such as rtphase.mac and rtphase.mnu.
rpl - Real-time polynomial baseline correctionrpl order
This command is obsolete in FELIX. has been replaced by macros that use modeless control panels. See macro files rtbasepoly.mac and rtbasepoly.mnu.
See alsopol - Polynomial baseline correction
rv - Read Varian filerv file_name
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 dependenceSymbols changedphase1 First-order phase angle
See alsorf - Read FELIX for Windows file
sar - Autoscreen commandsar ini opt
sar exe specID item symbol_score symbol_threshold
sar dsp matrix opt threshold
sar provides subcommands related to the Autoscreen module for SAR by NMR. Execution of this set of commands requires the Autoscreen license.
Symbol dependencesar 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 - Sinebell windowsb size shift
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 dependenceSee alsoqss - Skewed sinebell squared window
sca - Scale factor for dimensionsca dimension scale_factor
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.
sca -dimension scale_factor_variable
returns the current scaling in scale_factor_variable if the negative dimension is used for the dimension.
seg - Integral segmentsseg op arguments
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
sep - Separate real and imaginarysep
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 changedSee alsoalt - Alternating real/imaginary
set - Set work space to a valueset real 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
shl - Shift leftshl points
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 dependenceSee also
shr - Shift rightshr points
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 dependenceSee also
smo - Binomial smoothsmo times
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 alsoflf - FaceLift baseline correction
sp - Stack plotsp
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 dependenceSymbols changed
sqz - Squeeze a matrixsqz file threshold
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 - Set range to valuesrv first last real imaginary
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:set 1
ss 100 90
shr 600
srv 1 600 1defines 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 dependenceSee alsoset - Set work space to a value
ss - Sinebell squared windowss size shift
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 alsoqss - Skewed sinebell squared window
ssh - Signed shiftssh n1 n2 scale
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 dependenceSee also
ssp - Synthesize spectrum from peak listssp peaks
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 dependenceSee also
ste - Stella peak pickerste peak_entity pick_mode
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 dependenceminbok 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)
nextra extra points to increase by the peak box
outlev output level (0=quiet, 1=low, 2=medium, 3=high)
stb - Store work space to bufferstb buffer
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 dependenceSee alsopsh - Push the work space onto the buffer stack
ldb - Load buffer into work space
xsh - Exchange stack head with work space
sto - Store vector to matrixsto dim1 dim2 dim3 ...
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 dependenceSee alsoswb - Store work space to bundle
str - String manipulation operators
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.
str length string symbol
Return the length of the given string. The result is an integer greater than zero.
str sub string begin end symbol
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.
str index string substring symbol
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.
str match string matchstring symbol
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.
str parse string word_symbol cnt_symbol
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:
str parse `This is a string' word countyields the following symbols and symbol values:
count = 4 word1 = This word2 = is word3 = a word4 = stringstr parse (123.01,278.31) value count ().,parses based on blanks and the extra delimiters `().,' to yield:
count = 4 value1 = 123 value2 = 01 value3 = 278 value4 = 31Note that any ASCII characters may be used as delimiters. The blank is always a delimiter.
str exact string matchstring symbol
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 - Sub-string extractionsub text begin end symbol
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 alsorea - Read record from ASCII file
swb - Store work space to bundleswb
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 dependenceSee alsolwb - Load work space from bundle
sys - Execute system commandssys 'DOS_command'
sys puts you in touch with the command interpreter of the operating system. This command enables you to execute DOS commands with FELIX. The DOS_command must be single-quoted.
Note: Windows allows spaces in a file or folder name. To avoid the potential problems caused by spaces in file or folder names, you are advised to double-quote all symbols that hold file or folder names, as in the examples below:sys 'copy "&xxpath&xxfile" "&xxpath&yyfile"
sys 'del/f/q "&xxpath&xxfile"For your convenience, the following new subcommands are added to achieve the common file manipulations:sys del 'filename'
sys copy 'from_file' 'to_file'
sys rename 'from_file' 'to_file'
sys type 'filename'Since these subcommands are not executed through the DOS command, the filenames must be single-quoted, not double-quoted.
Executing a DOS command from FELIX opens an DOS window which is closed upon the compeletion of the command. If you want to see the text displayed in the DOS window, you can do something like the following:
sys 'dir > temp.txt'
sys type temp.txtThe first command issues a DOS command dir and redirect the output to a file temp.txt. The second command displays the content of temp.txt in the output window of FELIX for your review.
tex - Text annotationtex x0 y0 (z0 a0) (fix anchor) number text
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 dependencethick annotation text thickness
See also
til - Tile plottil 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.
til xpk tile_entity xpk_entity item# correlation tile_size
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.til atoms tile_ent spins spin_ent shift_ent tile_size
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.til pattern tile_ent pat_file spin_ent shift_ent tile_size
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.til off
til on tile_ent
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.til overlap tile_ent
overlap size
This operator combines overlapping tiles based on the overlap variable.
til reduce tile_ent dimension point
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.
til strip tile_ent
This operator allows you to make 2D strips from a 3D data set where each strip can be taken from a different plane.til who number
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
tim - A basic clock and chronographtim op symbol (symbol2)
tim provides some basic timer abilities. Most notably, you can time long processing macros.
tm - Trapezoidal multiplicationtm p1 p2 p3
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 - Type textty text
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 - Type a file of text to the usertyf file_name
tyf provides a way to put a large amount of text to the user with one command.See also
tym - Type text to motiftym text
tym displays a line of message on the status bar of the FELIX main window. It does not display the message in the text-port window. If you want to prevent the message from being overwritten, you should also use the ty command to display it in the text-port window..
unf - Unfold workunf
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 dependenceSymbols changed
ver - FELIX version number and release datever
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 - Integrate cross peak volumesvol peaks volumes slot ordinate
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
wa - Write an ASCII data filewa file_name
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 dependenceSee alsowr - Write a file (old format)
wn - Write a file (new format)
wai - Wait a whilewai time
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.wai -1 menufile
wai -1 menufile causes FELIX to pause the execution of the current macro until a modeless dialog box (defined by a menu file "menufile") is closed..
wm - Write macrowm file_name
wm writes the macro from the macro work space to a .mac file.Symbol dependenceSee also
wn - Write a file (new format)wn file_name
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 dependenceSee alsowr - Write a file (old format)
wr - Write a file (old format)wr file_name
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 dependenceSee alsown - Write a file (new format)
xpa - Cross-peak assignments from shifts and spinsxpa peaks spins shifts
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 alsoxps - Generate spins and shifts from cross peaks
xpk - Cross-peak operationsxpk 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 dependencehafwid cross peak half width factor
See alsoxpk who peaks d1_pt d2_pt ... symbol
xpk who peaks -1 symbol
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.xpk add peaks
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 peaks item
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.xpk edit peaks item symbol
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 peaks item dimen name
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.xpk volume peaks item symbol1 symbol2
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 peaks item1 item2 mode symbol
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 - Make a list of peaksxpl provides operators for creating item lists of cross peaks. For general information about lists, see Chapter 6., Database and tables. 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 dependencehafwid cross peak half width factor
frsize frame size (biggest list size)
nframe number of buffers (number of lists)
See alsoxpl box list# peaks lo1 hi1 ... loN hiN symbol
xpl box list# peaks -1 symbol
xpl box list# peaks 0 symbol
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 list# peaks lo1 hi1 ... loN hiN symbol
xpl touch_box list# peaks -1 symbol
xpl touch_box list# peaks 0 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 list# peaks lo1 hi1 ... loN hiN symbol
xpl inside_box list# peaks -1 symbol
xpl inside_box list# peaks 0 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.xpl point list# peaks pt1 ... ptN symbol
xpl point list# peaks -1 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 list# peaks dimen pt symbol
xpl line list# peaks -1 symbol
xpl line list# peaks 0 pt 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.xpl range list# peaks dimen lo_pt hi_pt 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 list# peaks dimen name symbol
xpl name list# peaks 0 name 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.xpl freq list# peaks dim freq_list resolution symbol
xpl freq list# peaks 0 freq_list resolution symbol
xpl freq list# peaks -1 freq_list# resolution symbol
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.
xpl pattern list# peaks dim pattern_# resolution spectrum_id 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.
xpl proto list# peaks dim proto_# resolution 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.
xpl clipboard list# peaks dim resolution 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.
xpl pt list# peaks dim assignment_pointer 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 list# peaks loppm1 hippm1 ... loppmN hippmN symbol
xpl box list# peaks 0 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 list# peaks loppm1 hippm1 ... loppmN hippmN 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 list# peaks loppm1 hippm1 ... loppmN hippmN 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.xpl pp list# peaks ppm1 ... ppmN 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 list# peaks dimen ppm 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.xpl pr list# peaks dimen loppm hippm 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.See alsofli - Frequency list manipulation
xps - Generate spins and shifts from cross peaksxps peaks spins shifts mode
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 alsobck - Back-calculate NOE intensities
xpa - Cross-peak assignments from shifts and spins
xsh - Exchange stack head with work spacexsh
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 dependenceSee alsoldb - Load buffer into work space
stb - Store work space to buffer
psh - Push the work space onto the buffer stack
xss - Simulated annealing assignment functionsxss build method experiment1 (experiment2 (experiment3)) spins_system_# (occurance) remove_intraspin_peaks iteration std_dev (htol) (ctol) output
xss pattern first_residue last_residue min_score discard store temp_fact iter_fact seq_fact output
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.
xss build method experiment1 (experiment2 (experiment3)) spin_system_# (occurance) remove iteration std_dev (htol) (ctol) output
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.
xss pattern first_residue# last_residue# min_score discard store temp_fact iter_fact seq_fact output
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.
xyl - Atom list manipulationThe 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 alsoxyl neighbors atom radius others list# symbol
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 atom list# 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.xyl atom atom radius others type list# symbol
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 atom list# 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 atom list# 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 center delta spectrum_id list# 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 center delta spectrum_id list# 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 frequency list# 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.
xyp - X,Y data pair manipulationIn 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 dependenceSymbols changedSee alsodr - Draw work space and stack
xyp zero
xyp zero zeroes the workspace, and changes the data type to (x,y) pairs.
xyp add x y sigma_y
xyp add adds a single data point to the work space.xyp delete x y
xyp delete deletes a single data point from the work space.xyp cursor add
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
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 pt# symbol_x symbol_y symbol_sigma
xyp get loads the values from a specified point number pt# into the symbols symbol_x, symbol_y and symbol_sigma.xyp label x_label y_label
xyp label specifies the label units for the x and y axis to be annotated on plots.xyp sort who order
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 file_name
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 file_name
xyp write writes the (x,y) pairs in the work space to an ASCII file with format as specified above.xyp fit function convergence parameters
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.xyp build function
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.
xyz - Atom manipulationThe 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 changedSee alsobck - Back-calculate NOE intensities
xyz draw sphere play
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 symbol
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.
xyz read type file
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.
xyz label atoms on/off redraw
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.xyz visible atoms on/off redraw
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.xyz color atoms pen redraw
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 atom1 atom2 symbol
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 atom1 atom2 pen redraw
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
xyz clear deletes all the entities connected to the molecule
xyz:atoms, xyz:bonds, xyz:residues, and xyz:atm_atr.xyz current type atoms bonds residues atom_atr patterns
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 entity_root file #_of_mol
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 - Zero workspaceze
ze causes the data in the workspace to be set to 0.0.
Symbol dependenceSee alsoset - Set work space to a value
zf - Zero fillzf points
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 dependenceSymbols changed
zgt - Zero greater thanzgt threshold
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 dependenceSee also
zi - Zero imaginaryzi
zi zeroes the imaginary part of the data in the workspace.
Symbol dependenceSee also
zlt - Zero less thanzlt threshold
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 dependenceSee also
zr - Zero realzr
zr zeroes the real part of the data in the workspace.
Symbol dependenceSee also
zp - Null plotThis command is similar to np, except that it does not draw the axis and labels.