Processing, visualization, and analysis interface (1D/2D/ND)

The processing, visualization, and analysis functions in FELIX are accessible throughout the interface.


File pulldown

The File pulldown (also accessed by simultaneously pressing the <Alt> and <f> keys on the keyboard, abbreviated as <Alt>+f) contains menu items for reading and/or saving datafiles, database files, and entities. It also contains menu items for importing spectrometer data, importing processed data, printing, and exiting the program. Each general menu item (command) in the File pulldown is described below.


File/New

The File/New command (<Alt>+fn):

FELIX displays a control panel with a list of the files in the database or matrix directory. Select the desired type (File Type):  either database or matrix. Enter the name of the file in the Selection box. To build a matrix, set up the sizes and select the appropriate dimension.


File/Open

Use the File/Open command (<Alt>+fo or <Ctrl>+o) to perform these tasks:

FELIX displays a control panel with a list of the files in the data, matrix, molecule, or macro directory. Select the desired file by clicking the filename or by typing in the name. The NMR datafiles can be in any of these formats:

To read in FELIX old-format data, change the Format to Old Format. The default is New Format for FELIX datafiles.

If you choose to open an existing database file for storing spectral information and a database is currently open, FELIX closes the current database and opens the newly selected one. If the first database has changed in some way, once you select the new database, FELIX prompts you to save or discard the changes to the first database before closing it.


File/Save

Use the File/Save command (<Alt>+fs) to save the current database or the current data in the workspace to disk. If the file already exists, FELIX prompts you to quit or overwrite the file.


File/Save As

Use the File/Save As command (<Alt>+fa) to save the current database, the current data in the workspace, the current matrix, or theoretical matrix to disk with a new name. If the file already exists, FELIX prompts you to quit or overwrite the file. The new database now becomes the current database.


File/Close

Use the File/Close command (<Alt>+fc) to close the current database, the current data in the workspace, or the current matrix. For a write-enabled matrix, FELIX stores the current parameters (displayed limits, display type, current entities) in the header. FELIX uses these parameters the next time you open this matrix to set the limits, display color, peak, and other entities.


File/Import

Use the File/Import (<Alt>+fi) command to generate a pullright menu of controls used to import database entities of tables, including a generic table-import command and some special table-import commands.

Table

Use the File/Import/Table (<Alt>+fit) command to read an ASCII file from disk into the binary FELIX database.

Note: This action is very format-specific. The entity file you read must be in an acceptable format. Use Selection to select an ASCII table file. Use Table Name to specify an entity that will be created in the database file.

Peaks

Use the File/Import/Peaks command (<Alt>+fip) to read an ASCII file that contains peak information into the peak entity. FELIX prompts you to specify an input filename as well as an entity name. Supported formats include:

Plot Limits

Use the File/Import/Plot Limits command (<Alt>+fil) to read and redefine the plot limits on the current matrix displayed. The file you read in should have been exported earlier using the File/Export/Plot Limits command.


File/Export

Use the File/Export (<Alt>+fe) command to open a pullright menu of controls to export database entities of tables. These controls include a generic table-export command and some special table-export commands.

Table

Use the File/Export/Table (<Alt>+fet) command to write a FELIX database entity to an ASCII file on disk. In the first control panel, select an existing entity. In the next control panel, enter an ASCII table file as the Selection.

Peaks

Use the File/Export/Peaks command (<Alt>+fep) to write the peak entity into an ASCII file that contains peak information. FELIX displays the file contents in a text window.

FELIX prompts you to specify a filename as well as the current peak entity name. The supported formats include:

Plot Limits

Use the File/Export/Plot Limits command (<Alt>+fel) to write out the current plot limits of the displayed matrix.


File/Convert

Use the File/Convert (<Alt>+ft) to open a pullright menu of converting (filtering) controls. FELIX converts only processed matrices.

Matrix

Use the File/Convert/Matrix (<Alt>+ftm) command to convert processed spectrometer data from formats that FELIX can filter (translate) into the FELIX matrix format. This makes a new FELIX matrix, which can later be read into the program. These formats are supported:


File/Print Setup

Use the File/Print Setup command (<Alt>+fr) to set up the printer and other properties of the printing job.


File/Print Preview

Use the File/Print Preview command (<Alt>+fv) to preview the plot.


File/Print

Use the File/Print command (<Alt>+fp) to open a hardcopy plot of the spectra in the current frame.

Note: FELIX uses the same parameters for screen displaying and hardcopy plotting. To control the size and location of the spectral plot on the paper, select Preference/Plot Parameters; next, click the Place button.


File/Licenses

Use the File/Licenses command (<Alt>+fl) to release any features that you don't currently need, allowing others in your workgroup to use them. Also, if one feature is being used by another concurrent user of FELIX when you started FELIX but becomes available later in your session, select this function to use the feature in your session.


File/Log File

Use the File/Log File/Open command (<Alt>+ffo) to open a log file, which will record the FELIX commands executed from this point.

Use the File/Log File/Close command (<Alt>+ffc) to close a log file and terminate the recording of the FELIX commands executed.

Use the File/Log File/Replay command (<Alt>+ffr) to open a log file and repeat the commands recorded in the log file.


File/Exit

Use the File/Exit command (<Alt>+fx) to exit FELIX. If changes have been made to the FELIX database, a FELIX dialog box prompts you to Save the database and exit and to Save the current environment (which can be restored later).


View pulldown

The most common way to manipulate displays is to access the View pulldown.


View/Plot

Use the View/Plot command (<Alt>+vp or <Ctrl>+p) to redraw the current workspace.


View/Plottype

To select a type of plot other than the current one, select the View/ Plottype command (<Alt>+vt). Alternatively, you can select from the combo box in the main tool bar.

FELIX displays NMR data in the following ways:

1D

FELIX presents the 1D data values in the workspace.

Intensity plots

In the intensity plot, FELIX presents data values above a set contour level as a filled rectangular region.

The intensity plot is drawn more quickly and coarsely than a contour plot. It is useful for uncritical examinations of the data; for example, when you are adjusting the contour levels or selecting a region for display as an expanded contour plot.

Contour plots

The contour plot displays the data as closed lines that follow adjacent data points of a set value. In other words, each closed contour line is the cross-section of a peak taken at a set value. Contour plots display the matrix in the most precise form and are used for data analysis.

Null

FELIX erases the plot and leave it blank.

Overlay plots

The contour plot displays the data as closed lines that follow adjacent data points of a set value. In other words, each closed contour line is the cross-section of a peak taken at a set value. Contour plots display the matrix in the most precise form and are used for data analysis.


View/Tile and Strip Plot

In addition to the standard plot types for ND data, FELIX can produce tile plots. A typical plot shows a matrix region as several small peaks separated by much space. A tile plot eliminates the intervening space and shows the peaks in much greater detail. This allows FELIX to displays features that are far apart in the actual matrix t on a single plot.

A special tile plot in which one of the axes runs across the full spectrum is a strip plot. To turn these types of plot on and off, use the View/Plottype/Tile/Strip Plot toggle.


View/Limits

The items in the Limits menu provide numerous options for quickly changing the expansion limits.

Set Limits

Use the View/Limits/Set Limits command (<Alt>+vls or <Ctrl>+s) to specify the spectral limits in real time. When you select this command, FELIX displays a small crosshair cursor. Move this cursor to the region you want to expand and drag out the region to be expanded. FELIX displays the expanded plot when you release the mouse button. If you select too small a region (fewer than four data points in any dimension), FELIX assumes that you accidentally pressed and released the mouse button without selecting a region and displays a warning message without changing the plot limits.

Manual Limits

Use View/Limits/Manual Limits command (<Alt>+vlm) to expand the plot to specific values for the limits in either ppm or points. If you have a 3D or 4D spectrum, specifying 1D limits (or 2D limits for a 4D spectrum) as one point allows you to plot a plane instead of a cube.

Full Limits

Use the View/Limits/Full Limits command (<Alt>+vlf or <Ctrl>+f) to restore the full spectrum display.

Last Limits

Use the View/Limits/Last Limits command (<Alt>+vll) to redisplay the plot with the previous limits. Use this command to rapidly restore an expanded plot.

Transpose Limits

Use the View/Limits/Transpose Limits (<Alt>+vlt>) command to exchange the current horizontal plot limits with the current vertical plot limits. FELIX switches the limits and redraws the plot. This is an easy way to jump to the symmetry-related region in a homonuclear 2D matrix or a homonuclear part of a 3D or 4D matrix.

Order of Plot

Use the View/Limits/Order of Plot (<Alt>+vld) command to control the order in which the matrix dimensions appear on the display. By default, D1 is plotted along the x axis, and D2 is plotted along the y axis. When you select this command, FELIX displays a control panel where you specify the plot order.

D1 - D2 specifies that the plot be ordered with D1 along the x axis and D2 along the y-axis

D2 - D1 specifies that the plot be ordered with D2 along the x axis and D1 along the y axis.


1D vector views

If you have displayed a 2D, 3D, or 4D matrix you can select 1D vectors using the following set of commands.

1D Horizontal

Use the View/Limits/1D Horizontal (<Alt>+vlr) command to select a row from the matrix for viewing as a 1D vector plot. Select the row using a horizontal line cursor by moving the cursor over the desired row and clicking the left mouse button. FELIX loads the selected row into the 1D workspace and plots it in the display. The plottype popup on the iconbar changes to 1D.

1D Vertical

Use the View/Limits/1D Vertical (<Alt>+vli) command to select a column from the matrix for viewing as a 1D vector plot. Select the column using the vertical line cursor. FELIX loads the selected column into the 1D workspace and plots it in the display. The plottype popup on the iconbar changes to 1D.

1D Orthogonal

Use the View/Limits/1D Orthogonal (<Alt>+vlg) command to select a 1D slice that is orthogonal to the current 2D slice of the 3D or 4D matrix for viewing as a 1D vector plot. Select the slice using the crosshair cursor by moving the cursor over the desired spot and clicking the left mouse button. FELIX loads the selected slice into the 1D workspace and plots it in the display. The plottype popup on the iconbar changes to 1D. For a 4D spectrum the slice runs along the third (order3) dimension.

1D Orthogonal 2

Use the View/Limits/1D Orthogonal 2 (<Alt>+vln) command to select a 1D slice that is orthogonal to the current 2D slice of the 4D matrix for viewing as a 1D vector plot. Select the slice using the crosshair cursor. FELIX loads the selected slice into the 1D workspace and plots it in the display. The plottype popup on the iconbar changes to 1D. The slice runs along the fourth (order4) dimension.


2D plane views

If you have displayed a 3D or 4D matrix you can select 2D planes for viewing using the following set of commands.

Real-time Plane

The View/Limits/Real-time Plane (<Alt>+vl-) command brings up the plane-selection slider and lets you view a 2D plane from a 3D or 4D spectrum.

Select Plane

By using the View/Limits/Select Plane (<Alt>+vlp) command you can specify a 2D plane for display. A FELIX control panel prompts you to specify the matrix slice. Select the switch beside the plane that interests you. Enter the value of the point or ppm value for the specific plane in the corresponding box. Set whether ppm or point should be used. Then, select OK; FELIX displays the requested 2D slice.

Horizontal Plane

The View/Limits/Horizontal Plane (<Alt>+vlh) command lets you use a cursor to select a slice that is orthogonal and oriented horizontally relative to the current 2D slice of a 3D or 4D spectrum. Selecting this command prompts FELIX to display a horizontal line cursor. Click the desired line on the currently displayed 2D slice to display the selected orthogonal slice in the frame.

The item in the pulldown menu has a variable directionality connected, that is, if a D1-D2 plane is current, the command appears as Horizontal Plane (D1-D3).

For a 4D matrix, use the View/Limits/Horizontal 2 Plane (<Alt>+vlz) command to select along the other orthogonal direction. For example, if your current display is D1-D2, then both a Horizontal Plane (D1-D3) and a Horizontal 2 Plane (D1-D4) command are available).

Vertical Plane

Use the View/Limits/Vertical Plane (<Alt>+vlv) command to use a cursor to select a slice that is orthogonal and oriented vertically relative to the current 2D slice of a 3D or 4D matrix. FELIX display a vertical line cursor. Click the desired line on the currently-displayed 2D slice; FELIX displays the selected orthogonal slice in the frame.

The item in the pulldown menu has a variable directionality connected, that is, if a D1-D2 plane is current, the command appears as Vertical Plane (D1-D3).

.For a 4D matrix, an additional command (View/Limits/Vertical 2 Plane (<Alt>+vlz)) enables you to select along the other orthogonal direction (for example, if your current display is D1-D2, then both a Vertical Plane (D1-D3) and a Vertical 2 Plane (D1-D4) command are available).

Orthogonal Plane

Use the View/Limits/Orthogonal Plane (<Alt>+vlo) command to use a cursor to select a slice that is orthogonal relative to the current 2D slice of a 4D matrix. FELIX displays a crosshair cursor. Click the desired spot on the currently displayed 2D slice to display the selected orthogonal slice in the frame.

The item in the pulldown menu has a variable directionality connected. That is, if a D1-D2 plane is current, the command appears as Orthogonal Plane (D3-D4).


View/Export Limits

You can redefine limits in the current frame as with the previous View/Limits commands, and you can also define new limits in another frame using the View/Export Limits (<Alt>+ve) commands, as described below.

Export Limits

The View/Export Limits/Export Limits (<Alt>+vee) command allows you to export the plot limits from the current frame to another frame.

Export Reference

The View/Export Limits/Export Reference (<Alt>+vef) command allows you to export the spectral reference parameters from the current frame to another frame.

Export 1D Horizontal

The View/Export Limits/Export 1D Horizontal (<Alt>+ver) command lets you select a row from the matrix for viewing as a 1D vector plot in another frame. Select the row using the horizontal line cursor. FELIX loads the selected row into the 1D workspace and plots it in the selected frame. The frame where the new slice is to be displayed should already exist.

Export 1D Vertical

The View/Export Limits/Export 1D Vertical (<Alt>+vei) command allows you to select a column from the matrix for viewing as a 1D vector plot. Select the column using the vertical line cursor. FELIX loads the selected column into the 1D workspace and plots it in the selected frame. The frame where the new slice is to be displayed should already exist.

Export 1D Orthogonal

The View/Export Limits/Export 1D Orthogonal (<Alt>+veg) command allows you to select a 1D slice that is orthogonal to the current 2D slice of the 3D or 4D matrix for viewing as a 1D vector plot. Select the slice using a crosshair cursor by clicking the desired spot. FELIX loads the selected slice into the 1D workspace and plots it in the selected frame. The frame where the new slice is to be displayed should exist. For a 4D spectrum, the slice runs along the third (order3) dimension.

Export 1D Orthogonal 2

The View/Export Limits/Export 1D Orthogonal 2 (<Alt>+ven) command allows you to select a 1D slice that is orthogonal to the current 2D slice of the 4D matrix for viewing as a 1D vector plot. Select the slice using the crosshair cursor by clicking the desired spot. FELIX loads the selected slice into the 1D workspace and plots it in the selected frame. The frame where the new slice is to be displayed should exist. The slice runs along the fourth (order4) dimension.

Export 1D Transposed

The View/Export Limits/Export 1D Transposed (<Alt>+vet) command allows you to select a 1D slice that is orthogonal to the current 2D slice of the 3D matrix for viewing as a 1D vector plot. Select the slice using the crosshair cursor by clicking the desired spot. FELIX loads the transposed position slice into the 1D workspace and plots it in the selected frame. The frame where the new slice is to be displayed should exist. This feature can be useful for analysis of a 3D HCCH-TOCSY spectrum where you can display an H-H plane along a 13C frequency. Clicking, for example, a Ha-(Ca)-Hb peak can give a 13C slice at the Hb-Ha position, allowing you to locate the Cb frequency.


2D plane exporting

If you have displayed a 3D or 4D matrix, you can export 2D planes to a different frame using the following set of commands.

Export Horizontal

The View/Export Limits/Export Horizontal (<Alt>+veh) command lets you use a cursor to select a slice that is orthogonal and oriented horizontally relative to the current 2D slice of a 3D or 4D spectrum. Selecting this command prompts FELIX to display a horizontal line cursor. Click the desired line on the currently displayed 2D slice to display the selected orthogonal slice in the selected frame. The frame where the new slice is to be displayed should exist.

The item in the pulldown menu has a variable directionality connected, i.e., if a D1-D2 plane is current, the command appears as Export Horizontal (D1-D3).

For a 4D matrix use the View/Export Limits/Export Horizontal 2 (<Alt>+vez)) to select along the other orthogonal direction. For example, if your current display is D1-D2, both an Export Horizontal (D1-D3) and an Export Horizontal 2 (D1-D4) command are available.

Export Vertical

The View/Export Limits/Export Vertical (<Alt>+vev) command lets you use a cursor to select a slice that is orthogonal and oriented vertically relative to the current 2D slice of a 3D or 4D matrix. Selecting this command prompts FELIX to display a vertical line cursor. Clicking the desired line on the currently displayed 2D slice prompts FELIX to display the selected orthogonal slice in the selected frame. The frame where the new slice is to be displayed should exist.

The item in the pulldown menu has a variable directionality connected, i.e., if a D1-D2 plane is current, the command appears as Export Vertical (D2-D3).

For a 4D matrix use the View/Export Limits/Export Vertical 2 (<Alt>+ve2) command to select along the other orthogonal direction. For example, if your current display is D1-D2, both an Export Vertical (D2-D3) and an Export Vertical 2 (D2-D4) command are available.

Export Orthogonal

The View/Export Limits/Export Orthogonal (<Alt>+veo) command lets you use a cursor to select a slice that is orthogonal relative to the current 2D slice of a 4D matrix. Selecting this command prompts FELIX to display a crosshair cursor. Clicking the desired spot on the currently displayed 2D slice displays the selected orthogonal slice in the selected frame. The frame where the new slice is to be displayed should exist.

The item in the pulldown menu has a variable directionality connected, i.e., if a D1-D2 plane is current, the command appears as Export Orthogonal (D3-D4).

Export Transposed

Use the View/Export Limits/Export Transposed (<Alt>+ved) command to use a cursor to select a slice that is transposed relative to the current 2D slice of a 3D matrix. FELIX displays a crosshair cursor. Click the desired spot on the currently displayed 2D slice; FELIX loads an orthogonal 1D slice which is also transposed.

Then FELIX searches through that 1D slice to find the largest peak and uses that peak to define a new plane, which is then displayed in the selected frame. This is useful for the analysis of a 3D HCCH-TOCSY spectrum where you would display an H-H plane along a 13C frequency. Clicking, for example, an Ha-(Ca)-Hb peak initiates a search for the 13C slice at the Hb-Ha position, allowing you to locate the Cb frequency and export the Hb-(Cb)-Ha plane. The frame where the new slice is to be displayed should be open.


View/Draw Peaks

Use the View/Draw Peaks (<Alt>+vd or <Ctrl>+k) command to display the 1D peaks on a 1D spectrum or the ND cross-peak footprints represented by the current 1D peak or ND cross-peak entity, according to the parameters specified using the Preference/Peak Display command. Set the toggle on to display the peaks after every spectrum plot.


View/Draw Frequencies

Use the View/Draw Frequencies (<Alt>+vf) command to display the frequencies in the frequency buffer as horizontal and vertical lines through the 2D plane, according to the parameters specified using the Preference/Frequency Display command. Set the toggle on to display the frequencies after every spectrum plot.


View/Draw Integrals

Use the View/Draw Integrals (<Alt>+vs) command to display the integrals on a 1D spectrum, according to the parameters specified using the Preference/Integral command. Set the toggle on to display the integrals after every 1D plot.


View/Draw Basepoints

Use the View/Draw Basepoints (<Alt>+vb) command to display the picked baseline points on a 1D spectrum. Set the toggle on to display the points after every spectrum plot.


View/Draw Annotations

Use the View/Draw Annotations (<Alt>+va) command to display the annotations in the current annotation file (annfil). Set the toggle on to display the annotations after every spectrum plot.


View/Draw 1D Slices

Use the View/Draw 1D Slices (<Alt>+v1) command to specify 1D sections (horizontal, vertical, or both) to export to a different frame (or frames) interactively using the cursor or slider(s) from the current matrix. FELIX prompts you to specify which dimension(s) to take the 1D slices from and which frame(s) is the target to export the slices. FELIX draws a line on the parent plot showing the location from which the slice was extracted.


View/Draw Multiple 1D Slices

Use the View/Draw Multiple 1D Slices (<Alt>+vm) command to specify multiple 1D sections (either horizontal or vertical) to export to a different frame interactively, using the cursors. FELIX draws the selected slices on top of each other in a stack. FELIX prompts you to specify which dimension to take the 1D slices from. FELIX draws lines on the parent plot showing the location from which the slices were extracted.


View/Draw Thick 1D Slice

Use the View/Draw Thick 1D Slice (<Alt>+vk) command to specify a block of 1D slices (either horizontal or vertical) using a rubber band box, and export the sum of them to a different frame. FELIX prompts you to specify which dimension to take the 1D slices from and which frame is to export the results to.


View/Draw 2D Slices

Use the View/Draw 2D Slices (<Alt>+v2) command to specify 2D sections to export from the current 3D or 4D matrix to different frames interactively, using the cursor. FELIX prompts you to specify which dimensions to take the 2D slices from and the target frames to export the selected 2D sections. FELIX draws a line on the parent plot showing the location from which the slice was extracted.


View/Tile Plot

FELIX display a tile plot as a large rectangular layout of small rectangular tiles, precisely aligned with each other. Each tile is actually the intersection of a narrow region along D1 and a narrow region along D2. A tile plot that is three tiles across and four tiles tall is the result of three regions along D1 intersecting with four regions along D2. The unit of interest is always a line segment, or region, in a single dimension; while the tile plot illustrates the intersections of these segments.

FELIX stores every tile as an entity in the database. The format of the entity is a set of line segments for each dimension, where the segment endpoints are recorded in data-point units. When you build a tile plot, FELIX reads the tile entity to determine which regions to tile.

Use the View/Tile Plot (<Alt>+vi) command to open a pullright menu of tile controls, which are described below.

Tile Plot

Use the View/Tile Plot/Tile Plot command (<Alt>+vie) to toggle the tile plot on or off. Use this function after a tile entity is defined with, for example, the Tile One Peak or Tile Regions command.

Tile One Peak

Use the View/Tile Plot/Tile One Peak (<Alt>+vip) command to create a tile entity and plot from a chosen cross peak. Select a cross peak from which to generate a tile plot with the crosshair cursor.

The peak's footprint defines the first two line segments. FELIX searches in the peak entity for all other peaks that align with the chosen peak. Each of the other peaks contributes at least one line segment to the new tile entity. The resulting tile plot shows all the regions in the matrix where these segments intersect. Use the View/Tile Plot/Tile Plot Parameters command to set alignment criteria.

Tile Regions

Use the View/Tile Plot/Tile Regions (<Alt>+vir) command to create a tile entity and plot from a user-generated set of regions. Use the small crosshair cursor to select a rectangular region. Each such region defines up to two line segments for the tile entity. Drag out additional regions to define more segments. Click the <Esc> key to quit selecting regions. The resulting tile plot shows all the regions in the matrix where these segments intersect. FELIX combines segments that are almost identical (those with significant overlap).

Tile Spin System

This menu item can be used only in conjunction with Assign; i.e. you must have an Assign project set up before you can use this command. Here you can define a tile plot using any combination of frequency clipboards, protopatterns, and patterns.

Tile ROIs

Use the View/Tile Plot/Tile ROIs command to create a tile entity and plot from a user-defined region of interests (ROIs).

Delete One Column, Delete One Row

A tile plot may have too many line segments, so that the display shows regions that are not of interest. Use the View/Tile Plot/Delete One Column (<Alt>+vio) and View/Tile Plot/Delete One Row (<Alt>+vid) commands to manually remove a single line segment from the entity to generate a new tile plot with fewer tiles. Use the half-crosshair cursor to delete a line segment from the entity. FELIX then displays the new reduced tile plot.

Tile Plot Parameters

Use the View/Tile Plot/Tile Plot Parameters (<Alt>+vit) command to open a control panel that affects many facets of tile plot creation and display. Set the following criteria here:

Cross-peak alignment can be measured in terms of footprint correlation or line shape correlation, and you can set the correlation threshold to control which peaks are considered aligned.


View/Strip Plot

Strip Plot

Use the View/Strip Plot/Strip Plot command (<Alt>+vrr) to change a strip plot to a regular plot, or to turn on a previously defined strip plot from a regular plot.

Strip Plot of Clipboard

The View/Strip Plot/Strip Plot of Clipboard menu item (<Alt>-vrc) generates a strip plot representation from the current frequencies in the clipboard.

/Strip

The View/Strip Plot/Strip Plot of Protopattern menu item (<Alt>-vrp) generates a strip plot representation from the current frequencies in the selected prototype pattern.

Strip Plot of Spin System

The View/Strip Plot/Strip Plot of Spin System menu item (<Alt>-vrs) generates a strip plot representation from the current frequencies in the selected patterns (spin system).

Make One Horizontal Strip

Use the View/Strip Plot/Make One Horizontal Strip command (<Alt>+vrh) to create a 2D slice in which the y dimension contains all the points and the region covered by the x dimension is defined by the cursor horizontal strip.

Make One Vertical Strip

Use the View/Strip Plot/Make One Vertical Strip command (<Alt>+vrv) to create a 2D slice in which the x dimension contains all the points and the region covered by the y dimension is defined by the cursor vertical strip.

Make One Orthogonal Strip

Use the View/Strip Plot/Make One Orthogonal Strip command (<Alt>+vro) to draw a single strip that is orthogonal to the current 2D plot of a 3D or 4D spectrum.

Define the coordinates and width of the strip plot by dragging the desired area.If you drag horizontally, the short side of the strip will be the horizontal axis; if you drag vertically, the short side of the strip will be the vertical axis. FELIX zooms the plot according to the starting and ending position of the cursor. The long axis of the strip plot will be the current orthogonal dimension.

Scale Strip Plot

Use the View/Strip Plot/Scale Strip Plot command (<Alt>+vrs) to redefine and correct the scaling of too-thin strip plots.


View/Overlay

The View/Overlay command is used to overlay 2D views of multiple 2D, 3D, or 4D matrices. When you execute the View/Overlay command this brings up the Overlay Matrices table. This table is used to add matrix files to the set of available matrices and to control how the matrix files are viewed. Position the table at an appropriate location in the FELIX window so that you can view both the active frame and the table simultaneously. Activate the table by clicking on its top menu bar to highlight it. This causes FELIX to display the table commands and table icons. At any time you can switch back to the normal FELIX commands and icons by clicking on the top menu bar of the Frame 1 window to activate it.

To add matrices to the table, first click on the table to highlight it. Then use one of the commands in Edit/Add Experiment (from the table commands) to select and add a matrix. Repeat this process to add all desired matrix files. As you add each experiment the program pauses and allows you to adjust the display settings for the matrix. Highlight the Frame 1 window if needed and use the FELIX menu commands to adjust the contour level and color scheme. For example, you can click on the Plot Parameters icon to bring up the Plot Parameters menu to adjust most display attributes. When the matrix display is correct click Accept to add the matrix to the table. Continue this process for each new matrix file.

When all matrix files have been added, highlight the table to make sure that the table commands are available. You can display an individual matrix file by double-clicking on the appropriate row in the table or by selecting the row and clicking on the Draw Selected icon. To overlay multiple matrix files, select the desired rows in the table (using the shift and control keys as appropriate). Then click on the Overlay Multiple icon to draw the overlay display with the selected files. If you want to compare multiple files with the same base spectrum you can first define a base spectrum using the Preference/Preferences command and then use the Overlay Next and Overlay Previous icons to scan through the list.

Note that it is possible to display multiple 2D slices from the same 3D or 4D matrix by entering the same matrix multiple times. Each row in the table allows you to set the plane to view by adjusting the X_dim and Y_dim parameters which control the displayed orientation, as well as the Z_plane and A_plane parameters which control the particular point values in the other planes. In this way you can select both the view orientation and the particular slice to view.


View/Output

Use the View/Output command (<Alt>+vu) to open the output window again after it is closed. The output window is a docking window where the results, instruction, error and warning messages are displayed.


View/Command Input

Use the View/Command Input command (<Alt>+vc) to open the command input window after it is closed. The command input window allows you to issue FELIX commands or execute macros directly.


Edit pulldown

Use the items in this pulldown to view and edit entities in spreadsheet tables, delete entities, and add annotations to spectra.


Edit/Table

Use the Edit/Table command (<Alt>+et) to open any existing entity from the database in the spreadsheet viewer. Select the entity with the entity-selection tool.


Edit/Peaks

Use the Edit/Peaks command (<Alt>+ek) to open the current peak entity in the spreadsheet viewer. The table and the peak entity are interactively linked so that changes to the table (except for sorting) automatically change the peak entity; conversely, changes to the peak entity change the table.

The last column of the table (the intensities) are measured quantities; therefore, changing them in the table has no effect and is not reflected in the entity. The peak table interface has a set of special command and icons to streamline navigation in the spectrum and interaction with the peaks.

Note: The peak entity contains a different number of columns in different order than the spreadsheet.

Note: The entity differs from its view in the spreadsheet, since patterns are stored in complex, multiply nested entities.


Edit/Delete Table

Use the Edit/Table Delete command (<Alt>+ed) to delete an entity (or table) from the database. Select the entity with the entity-selection tool.

Note: Closing the spreadsheet view of an entity does not remove that entity from the database. Use Edit/Table Delete to delete it.


Edit/NOE_Distance

The Edit/NOE_Distance menu item (<Alt>-en) opens the current NOE distance-restraint entity in the spreadsheet viewer. The restraint table interface has a set of special menu items and icons that streamline navigation in the spectrum and interaction with the restraints.


Edit/3J Restraints

The Edit/3J Restraints menu item (<Alt>-e3) opens the current 3J dihedral restraint entity in the spreadsheet viewer. The restraint table interface has a set of special menu items and icons to streamline navigation in the spectrum and interaction with the restraints.


Edit/Prototype Patterns

The Edit/Prototype Patterns menu item (<Alt>-ep) opens the current prototype pattern entity in the spreadsheet viewer, but can be accessed only if you have activated the Assign module and built an Assign project. The protopattern table interface has a set of special menu items and icons to streamline navigation in the spectrum and interaction with the prototype patterns.

Note: The number and headings of columns in the prototype pattern entity are different from those in the spreadsheet.


Edit/Spin Systems

The Edit/Spin Systems menu item (<Alt>-es) opens the current pattern or spin-systems entity in the spreadsheet viewer, but can be accessed only you have activated the Assign module and built an Assign project. The spin-system table interface has a set of special menu items and icons to streamline navigation in the spectrum and interaction with the patterns.

Note: The entity differs from its view in the spreadsheet, since patterns are stored in complex, multiply-nested entities.


Edit/Stretches

The Edit/Stretches menu item (<Alt>-ec) opens the current stretch of the spin systems entity in the spreadsheet viewer, but can be accessed only if you have activated the Assign module and built an Assign project. The stretch table interface has a set of special menu items and icons to streamline navigation in the spectrum and interaction with the stretches.


Edit/Residues

The Edit/Residues menu item (<Alt>-er) allows you to view the assignment status of each residue in the spreadsheet viewer, that is, which pattern and which frequency are assigned to which residue and which atom. You can access only this menu item if you have activated the Assign module and built an Assign project.


Edit/Atoms

The Edit/Atoms menu item (<Alt>-eo) allows you to view the current atoms entity in the spreadsheet viewer, but can be accessed only if you have activated the Assign module and built an Assign project.


Edit/Annotation

You may add annotations to any flat graphics plot, whether a simple 1D spectrum, a 2D spectrum, or a 2D slice of an N-dimensional matrix.

Annotation positions are specified in normalized device coordinates set on the current plot. The bottom-left and top-right corners of the current plot have coordinate values (0,0) and (1,1), respectively. The menus always place spectral annotations with respect to the current plot. If the spectrum dimensions differ from those used when the original annotations file was created, the annotation items will not be displayed correctly on the new plot with respect to the existing cross peak and spectrum lines. In this case, you must create an entirely new annotation file; or, you must edit the old one to obtain the desired placement of these items.

FELIX saves the annotations as commands in an ASCII file with an extension of .ann. If the current frame has not been associated with an annotation file, use the Edit/Annotation (<Alt>+ea) command to select an existing annotation file or create a new one. Otherwise, FELIX prompts you to select from three options:

If an annotation file is open, FELIX displays a modeless control panel; use the annotation commands within it to add, move, and delete various annotations. To exit the annotation interface and save your file, select Done at the bottom to accept the changes, or select Cancel to discard the changes you've made.

Short descriptions of items in the Annotations control panel are given in Table 6.


Preference pulldown


Preference/Plot Parameters

This menu item (command) sets various display parameters that affect the plotting of spectrum data.

Note: Various items appear on this menu, depending on whether the data is 1D or ND.

For 1D data the parameters are divided among five control panels: Basic, Axis, Tick, Place, and Stack, which can be activated from each other by clicking the appropriate button

ND plot parameters

Similar to 1D data, plot parameters for ND data are divided among five control panels: Basic, Axis, Tick, Place and Stack.

The Basic control panel contains tools that control the appearance of the plotted matrix values. You can, for example, choose the base contour level to plot, the number of contour levels to plot, the level multiplier, and the colors of the contour levels.

The ND Plot Parameters-Axis control panel contains tools that control the appearance of the other portions of the plot - the axis units for each dimension, projection display, scale factors for each dimension, annotations, box around the plot, and grid lines.

The ND Plot Parameters-Tick control panel allows you to control the tick mark positions and axis text size for each dimension in a multi-dimensional data set.

Use the ND Plot Parameters-Place control panel to position the plot in the current FELIX frame.

Use the ND plot parameters-Stack control panel to change the settings for the stack plot.


Preference/1D Scale

As an alternative to control panel adjustment of 1D plotting parameters, FELIX offers a real-time interface that contains buttons and sliders to manipulate parameters. To activate this feature, select the Preference/1D Scale command (<Alt>+pe).

To adjust the spectrum's vertical scale, drag the Scale slider or enter a value to the box next to it. You can toggle between absolute and relative scaling. To adjust the vertical offset, click Offset; or, if there are multiple 1D slices to display, click Overlap to adjust the vertical overlap between them.

To specify any point's (peak's) vertical position, click the Set Scale button and click the cursor somewhere in the spectrum display. The point at that position will have the vertical value of the cursor.

To exit the dialog, click the OK button to accept the changes, or click the Cancel button to discard the changes.


Preference/2D/ND Levels

As an alternative to control panel adjustment of ND plotting parameters, FELIX offers a modeless dialog box to adjust the display. To access this interface, select the Preference/2D/ND Levels command (<Alt>+ps). You can adjust the Contour Threshold, the Number of Levels, and the Level Multiplier in real time. To exit click the OK button to accept the changes, or click the Cancel button to discard the changes.


Preference/Reference

To reference a spectrum, select the Preference/Reference command (<Alt>+pr). FELIX displays different control panels, depending on the dimensionality of the data.

1D spectrum referencing

The Reference 1D Data control panel prompts you for the referencing information:

1.   Set the Spectral Frequency and Spectral Width to the values of the spectrometer frequency in MHz and the spectral width in Hz.

2.   To enter the Reference Point value either type it into the box or click the Cursor button in the control panel. Then, move the vertical cursor to the desired reference point on the plot, and click the primary mouse button.

3.   FELIX displays the Reference 1D Data control panel again. Enter the reference value in the appropriate entry box, e.g., if you want axis units of Hertz, enter a reference value in the Reference Hertz box. For PPM units, enter a reference value in the Reference PPM box.

4.   Finally, click OK to close the panel and redisplay the data with the selected axis units.

ND spectrum referencing

The Reference Matrix control panel provides tools for referencing your matrix:

1.   Set the Axis type to PPM, None, Points, or Hertz.

2.   Next enter the Spectral Frequency in MHz, the Spectral Width in Hz, the Reference Point in data points, and the Reference Shift in PPM, then click OK.

3.   Use one of the three Cursor buttons to select the Reference Point for a displayed dimension.


Preference/Pick Parameters

When you select the Preference/Pick Parameters command, FELIX offers one of two different control panels, depending on the dimensionality of the data.

1D spectrum

Before picking peaks, set the threshold value manually or via the cursor.

Select the Cursor option in the popup and click OK to use a line cursor for selecting the peak-picking threshold on the plot.

Use Selection Mode to specify if you want only positive peaks, only negative peaks, or both.

Use Points, ppm, Hz, or Assignment to specify the peak table and the units that should be displayed on the peaks.

Use Draw Style to draw one-dimensional peak markers as lines, arrows, or line and arrows.

ND spectrum

This control panel provides access to the cross-peak entity (table), the cross-peak selection mode (positive peaks, antiphase peaks, negative peaks, and positive and negative peaks), and tools for specifying the antiphase search window size, fixed footprint sizes, and minimum and maximum halfwidth values.

Stella Peak Picker parameters

The general rule is that more example peaks means longer execution time: for a 2D matrix it can take up to several minutes to pick peaks using 6-10 example peaks. For 3D or 4D sets the time can be even longer.

A local maximum is picked as a peak if:

The definable parameters are:


Preference/Peak Display

Use the Preference/Peak Display (<Alt>+pd) command to control the appearance of the ND cross peak footprints. Here you set the display switch, the cross peak entity, and other relevant parameters:


Preference/DQF Parameters

Use the Preference/DQF Parameters (<Alt>+pa) command to choose an optimization method for the J-coupling measurement in DQF-COSY spectra (quasi-Newton, Simplex, or simulated annealing).


Preference/Keypad

Use the Preference/Keypad (<Alt>+pk) command to specify the small step size in points for <Alt>+keypad navigation.


Preference/Frame Layout

Use the Preference/Frame Layout (<Alt>+pf) command to specify the options for automatic frame arrangement. By default, whenever a new window (table or spectral) is open, FELIX automatically re-arranges the layout of the windows, with the tables tiled on the left side, occupying 20% of the main window area; and the spectral windows tiled on the remaining area of the main window.

You can turn off this feature by setting Action to None, or your can select another way to arrange the spectral frames, such as Cascade or Tile Horizontally. However, the table frames are always tiled in the designated area when automatically arranged. The location and size of the area to tile the table frames can be changed from the Table Layout parameters.

Note: You can manually call the automatic arrangement function by selecting the Window/Auto Arrange command.


Preference/Frame Connection

Use the Preference/Frame Connection (<Alt>+pc) command to connect and disconnect up to 12 frames containing different views of different spectra.

You can use this connection, for example, to view a 15N-1H HSQC spectrum in the primary frame and a 1H-1H view from the corresponding 15N-separated TOCSY and NOESY spectra in the two secondary frames, having the two secondary frames connected along each dimension and defining the plane selection direction in the HSQC spectrum to be along the 15N dimension. Therefore, looking at each HN-N peak in the HSQC spectrum, you can bring up the corresponding 15N plane in the TOCSY and NOESY spectra and visually collect each spin system quickly by hand.

You can also connect two frames, each containing a strip along an HN frequency from an HNCACB and a CBCACONH spectrum at the same 15N frequency. This permits a quick scan through the entire two 3D spectra to find the intra- and inter-residual CB-CA-N-HN.

Use the Custom option to select a trivial connection between two frames (D1 to D1 or D1-D2 to D1-D2) or specify a more elaborate one.

After a frame connection is set, use the Disable option to temporarily disconnect them. Use the Enable option to restore the connection.


Preference/Multiple Cursor

This command is similar to the Preference/Frame Connection command, in that you can connect and disconnect the cursors using the Preference/Multiple Cursor command (<Alt>+pu). You must specify which axis of one frame should share cursor positions with other frame's axis.


Preference/Table

Use the Preference/Table command (<Alt>+pt) to specify the current table (entity) names for peaks, integrals, volumes, and other items.


Preference/Directory

Use the Preference/Directory command (<Alt>+py) to display a control panel showing the current directory prefixes for each type of file that FELIX uses.

You can edit any box to change a file prefix. The file types that FELIX uses are listed in Table 18. The notation "read only" implies a sharable directory, while "read+write" denotes a directory that should be owned and used by only one person.


Preference/Memory

Use the Preference/Memory command (<Alt>+pm) to display a control panel showing the currently defined buffer size and the number of buffers allocated for FELIX. Here you can change the memory allocation.


Preference/Macro Debug

Use the Preference/Macro Debug command (<Alt>+pb) to display a control panel showing the options for debugging macros.

The latter two options provide you very useful ways to locate macros and menu files and trace errors.


Process1D pulldown


Process1D/DC Offset

Preventing baseline discontinuities

A problem you can encounter when zero filling time-domain data is related to baseline correction. If the right-most data points in the FID are significantly different from zero, and zero filling is performed, a discontinuity (step function) is introduced into the data. The spectrum resulting from the Fourier transformation of data that contain a step function has wiggles or waves in its baseline.

It is crucial to avoid discontinuities when zero filling badly truncated data. This common problem is encountered when processing multi-dimensional data, although it can be prevented by using baseline correction to remove DC offset.

Manipulation of time-domain data prior to Fourier transformation can be used to change the size and appearance of transformed spectra. In addition, some type of spectrum artifacts can be eliminated. Raw FIDs are usually corrected before Fourier transformation to remove any DC offset that may have occurred during data acquisition.

Setting baseline correction

To correct raw FIDs, select the Process1D/DC Offset (<Alt>+pd) command. FELIX displays a control panel. Set a baseline correction fraction to specify the fraction of the FID, starting from the right side, to be averaged to eliminate the DC offset. The default value of this symbol is 0.2, based on the assumption that most of the signal has decayed to zero in the last 20% of the FID. By averaging the last quarter or so of points in the FID, a good zero level can usually be defined. For complex time-domain data, which contain both real and imaginary parts, the DC offset for each part is calculated independently.

If the baseline-correction function can calculate an accurate zero level, the effect on the transformed spectrum will be to eliminate a spike at the observed frequency. However, if the data are badly truncated (not enough data points were collected), baseline correction may not be able to calculate an adequate zero level. In fact, by applying baseline correction you may add a DC offset. If you are worried that your data may be truncated but still want or need to baseline correct the DC offset in your FID, try baseline correcting using a smaller fraction of the FID; that is. set the value of the baseline correction-fraction to 0.05.


Process1D/Zero Fill

Use the Process1D/Zero Fill command (<Alt>+pz) to zero-fill spectra. Zero filling is commonly performed on time-domain data. By selecting the Process1D/Zero Fill / BC command, you may increase the number of points in the transformed spectrum and thereby increase the spectrum's apparent digital resolution. Zero filling a spectrum defaults to doubling the size of the data, but you may zero fill to any desired size.


Process1D/Solvent Suppression

Solvent signal suppression

NMR data are frequently composed of signals arising not only from resonances of interest, but also from the solvent used to dissolve the sample. Solvent signals may compromise the analysis of the signals of interest, and in extreme cases may completely obscure important spectrum features.

Although effective methods for minimizing the intensity of solvent signals at acquisition time exist, e.g., through tailored excitation, post-acquisition methods can be extremely useful when undesirable solvent signals persist.

FELIX offers three methods for reducing the intensity of such solvent signals: a linear prediction-based algorithm (LP), a convolution-based method (CNV), and a polynomial-based method.

LP-Based solvent suppression

The linear prediction-based solvent-reduction routine exploits a technical feature of the LP algorithm to estimate and remove contributions from the most intense components in the spectrum (the intensities of the signals present in the interferogram are effectively ranked). The algorithm relies on the fact that solvent resonance frequently represents the most intense component in the spectrum (as with data acquired in H2O) and explicitly assumes this as a part of its function. If the signal identified as the most intense component is not significantly larger (by default, 5 times the value of the other components), no solvent-peak elimination is done.

To access linear prediction-based solvent reduction, select the Linear Prediction option for Method in the Process1D/Solvent Suppression command. FELIX displays a control panel prompting you to specify the number of data points to use in the LP calculation and the number of signals to remove. A value of 1 for Signals To Remove eliminates only the most intense component of the spectrum, a value of 2 removes the two most intense components, and so on. If the signal identified as the most intense component is not significantly larger than the other components, no solvent-peak elimination occurs. You can view the results of solvent suppression and change the parameters interactively if you specify Real-Time for the Method.

CNV-based solvent suppression

The convolution-based solvent-reduction routine conducts a convolution of the data with a sinebell or Gaussian function to first identify the lowest-frequency component, and then subtracts that component from the data (Marion and Bax 1989).

Two parameters are available in this control panel: the convolution function, which can be either a sinebell or Gaussian function (which at best is largely an empirical issue) and the function width. The best value for the function width depends upon the widths of resonances in the spectrum and the resolution. In practice its value is empirically derived.

To access convolution-based solvent reduction, select the Time-Domain Convolution option for the Method parameter in the Process1D/Solvent Suppression command. FELIX displays a control panel prompting you to specify the convolution function type (sinebell or Gaussian), and the function width (the default value of 10 works well for 1H data acquired in 1-2 K data points). You can view the results of solvent suppression and change the parameters interactively if you specify Real-Time for the Method.

Polynomial-based solvent suppression

The polynomial-based solvent-suppression method uses a polynomial fitting method to remove solvent signals from the time-domain data. The solvent signal is approximated by calculating the mean value of groups of data points and fitting a polynomial to these mean values. The resulting function is then subtracted from the time-domain data. This technique works best when the solvent frequency is close to zero.

To access polynomial-based solvent suppression select the Polynomial option for the Method parameter in the Process1D/Solvent Suppression command. FELIX displays a control panel prompting you to specify the Points to Use and the Polynomial Order. The Points to Use represents the number of data points in each group of points to average. The Polynomial Order represents the order of the polynomial that is used to fit the set of average points. You can view the results of solvent suppression and change the parameters interactively if you specify Real-Time for the Method.


Process1D/Window Function

Time-domain NMR data can be multiplied by window functions that perform digital filtering to reduce noise or increase spectrum resolution. For example, the noise level in 1D NMR data can be attenuated by multiplying the FID by an exponential window function.

Use the Process1D/Window Function command (<Alt>+pw) to select a window function and adjust its parameters by entering parameters directly. You can also set the function interactively while FELIX displays plots of both the window function and the product of the FID (possibly the FT'd spectrum) and the window function.

Real-time adjustment

The available window functions are:

Once you select a window function, FELIX displays a new control panel. Enter the parameters and apply the selected window function, or select the real-time option.

If you select the real-time option, a real-time interface panel appears, which consists of three buttons and a group of sliders, depending on the window function. You can apply FT or draw only the FID using the options (No FFT/FFT/Bruker FT/Digital FT). You can also Reset the parameters to their original values.

When you finish viewing the window function, close the command by clicking Keep or Quit. These buttons close the real-time interface and either retain the FID as it appeared with the window function or restore the original FID without the window function applied, respectively.

Use the sliders to directly adjust the window function parameters in real time. For example, the real-time interface for the Sinebell window function has sliders for the Window Size and the Phase Shift. You can adjust these parameters by moving the cursor over the slider and dragging. The red slider bar moves and the updated value is displayed within the slider.

Since it is a modeless dialog, you can adjust the plot display through the main commands or the toolbar icons.

Window function descriptions

Matched filter is an automatic version of exponential multiplication that examines the FID and chooses an appropriate Lorentzian broadening. The matched filter calculates and applies a matched exponential window to the FID. The line broadening is calculated by performing a least-squares fit to the FID. If the FID has an extremely low signal-to-noise ratio, the fit may fail, and a message to that effect appears on the screen. Note that one large, narrow, softened resonance may dominate the fit. After applying the matched filter, FELIX sets the global line-broadening parameter to the value of the line broadening that was applied.

The matched filter command is useful because it allows FELIX to determine the optimal line-broadening parameter for your spectrum, and thus gives the best signal to noise ratios.

To access this function, select it from the interface or enter the following at the command line:

 > mf

For more detailed information, please see the mf command in the FELIX Command Language Reference Guide.

Convolution difference is an apodization function that calculates the difference between no line broadening and specified line broadening.

To access this function, enter at the command line:

 > cd lbroad

lbroad

Adjusts the convolution parameter for the exponential.

For more detailed information, please refer to the cd command in the FELIX Command Language Reference Guide.

To access this function, either select it from the interface or enter at the command line:

 > sb wsize wshift

wsize

Adjusts the number of data points for the window function.

wshift

Adjusts the phase shift of the window function.

To access this function, either select it from the interface or enter at the command line:

 > ss wsize wshift

wsize

Adjusts the number of data points for the window function.

wshift

Adjusts the phase shift of the window function.

To access this function, either select it from the interface or enter at the command line:

 > qsb wsize wshift wskew

wsize

Adjusts the number of data points for the window function.

wshift

Adjusts the phase shift of the window function.

wskew

Adjusts the skew of the window function.

To access this function, either select it from the interface or enter at the command line:

 > qss wsize wshift wskew

wsize

Adjusts the number of data points for the window function.

wshift

Adjusts the phase shift of the window function.

wskew

Adjusts the skew of the window function.

To access this function, either select it from the interface or enter at the command line:

 > em lbroad

lbroad

Adjusts the line-broadening parameter for the exponential.

To access this function, either select it from the interface or enter at the command line:

 > gm lbroad gbroad

lbroad

Adjusts the line-broadening parameter for the exponential.

gbroad

Adjusts the Gaussian parameter for the exponential.

To access this function, either select it from the interface or enter at the command line:

 > tm p1 p2 p3

p1

Adjusts the first point of the trapezoid.

p2

Adjusts the second point of the trapezoid.

p3

Adjusts the third point of the trapezoid.

To access this function, either select it from the interface or enter at the command line:

 > kw wsize alpha

wsize

Adjusts the number of data points for the window function.

alpha

Adjusts the alpha parameter of the Kaiser window.


Process1D/Linear Prediction

Linear prediction estimates the value of a point based on the values of adjacent points. This can be used to replace corrupted values in an FID or to extend an FID.

First-point prediction

The First Point Prediction command uses linear prediction to replace data values at the beginning of the FID. The Points to use tool in the control panel defines the number of points used to calculate the LP coefficients. A reasonable value for this parameter would be the number of points in the workspace minus the number of predicted points (the larger the setting of Points to use, the longer the action takes to complete). A good value for the Number of coefficients setting is one quarter to one third the value of Points to use. The Number of peaks is included for compatibility with older macros, but is not used in the calculation. The Number of points to predict specifies the point at which the First Points function begins predicting values. It estimates data values from that point backward to the first point of the FID. For example, to replace the values of the first three points of the FID with predicted values, enter a value of 3 for First Points.

Last-point prediction

Use the Last Point (or general) Prediction command to predict first points, extend the FID, or replace corrupted points.

Use the First Point parameter in the control panel to define the start of points used to calculate the LP coefficients.

Use the Last Point parameter to define the end of points to be used to calculate the LP coefficients.

Use the Start Point parameter to define the start of points to calculate.

Use the End Point parameter to define the end of points to calculate.

A good value for the Number of coefficients setting is one quarter to one third the value of points to be used for prediction. The four choices for the Method are Backward, Forward, Forward-Backward, and Mirror. Use root reflection by turning the Use Root Reflection parameter on. The Type of mirror LP is used only when the Method is set to Mirror. The 90-180 method is used when the data collection is delayed by one half the dwell time. The 0-0 method is used when there is no delay in the data collection.

LP calculation methods

You specify the method used to perform the LP calculation. The options include Forward, Backward, Forward-Backward, and Mirror Image.

When you use the Mirror Image technique, you can increase the Number of Coefficients to between one-half and two-thirds the value of the Points to use.

The Mirror Image technique requires prior knowledge of the phase of the data and nondecaying signals. Because of these restrictions, the Mirror Image technique is used primarily for severely truncated indirect dimensions of N-dimensional data sets when there is a need to calculate more LP coefficients than would be possible with the Forward- Backward method. The Mirror Image method includes options for data collected with no sampling delay and data collected with a one-half dwell time sampling delay.


Process1D/Transform

The commands under Process1D/Transform (<Alt>+st) apply to Fourier transformation, linear prediction, and Hilbert transforms in the workspace.

Complex FFT

The Complex FFT option applies a complex Fourier transform to the data in the work space. For this transform, the data must be true complex data, characterized by simultaneous sample and conversion of the real and imaginary signals.

Bruker FFT

The Bruker FFT option performs a complex Fourier transform on complex data that are unique to some Bruker spectrometers. These spectrometers cannot sample and convert the real and imaginary signals simultaneously; instead, they collect the real and imaginary signals alternately. If your data were collected in this mode, you must use the Bruker FFT option in the Process1D/Transform command.

Real FFT

The Real FFT option performs a real Fourier transform on real data in the work space. After the real Fourier transform, the data become complex with the spectrum in the real part of the work space.

Oversampled FFT

The Oversampled FFT option performs a complex Fourier transform on digitally oversampled data collected on Bruker DMX and newer-series spectrometers. If your data were collected using digital oversampling you should use this command to do the transform.

Inverse FFT

At times you may need to convert frequency-domain data into time-domain data. For this purpose, use the inverse Fourier transform. Select the Inverse FFT option in the Process1D/Transform command.

Hilbert transform

To perform a Hilbert integral transform on the data in the work space, select the Hilbert Transform option in the Process1D/Transform command. The Hilbert transform is valuable for creating a complex spectrum from a real spectrum; that is, it transforms real data in the frequency domain into complex data in the frequency domain. The Hilbert transform is required for rephasing a spectrum after the imaginary part is discarded, which can occur with multidimensional NMR data processing.


Process1D/Phase Correction

After Fourier transformation, a spectrum often appears to be out of phase . That is, the resonance lines appear to be a mixture of absorptive and dispersive shapes. This is due to several factors, including finite pulse lengths, acquisition delays, and analog filter response. NMR spectra can be phase-corrected after transformation by multiplying each data point value pair by a phase factor. You may also access this command with the hot keys <Alt>+sp.

Real-time phase correction

One of the most valuable features of FELIX is real-time phasing capability. To activate this feature, select the Real-Time option in the Process1D/Phase Correction command. FELIX displays a modeless dialog box with two sliders and some buttons. Since it is a modeless dialog, you may use the menubar commands or toolbar icons to adjust the display of the spectral plot.

The real-time phase interface includes two active slider bars. To adjust the current values for the zero-order and first-order phase corrections, drag the respective slider bars. The current values of the zero-order phase and the first-order phase are displayed above the sliders. The value ranges of the sliders are displayed beside them. To adjust the value ranges, type in a number directly followed by a carriage return. Or, click the Coarse or Fine buttons to increase or decrease the value ranges respectively.

To set the pivot for your spectrum, click the Pivot button. FELIX displays a vertical hair cursor. Move the cursor to where you want and click the primary mouse button. The current position of the pivot is indicated by a small red triangle at the bottom of your spectrum.

To return to the original phase values, click the Reset button. To quit the real-time interface and save and apply the phasing parameters, click OK. This updates the reserved symbols phase0 and phase1. To quit without saving the parameters, click Cancel.

Phase correction using parameters

In addition to using the real-time phase interface, you may also phase a spectrum by manually setting values for phase0 and phase1. Select Parameter as the Method in the Process1D/Phase Correction command.

The values in this control panel are updated when you exit the real-time phasing interface. To phase a spectrum manually, you must first define parameters for the zero-order correction (phase0) and the first-order correction (phase1). FELIX does not use a separate value for a spectrum pivot; instead, this is incorporated into the values of phase0 and phase1. To apply a phasing correction, update values for phase0 and phase1 in the control panel and click OK. To exit the control panel without applying or updating the phase parameters, click Cancel.

Note: When you repeatedly process similar spectra and want to apply a known set of phase corrections to a spectrum, it is easier to enter the phase corrections with this method than it is to re-phase a spectrum interactively in the real-time phasing interface.

Automatic phase correction

In addition to the phasing techniques described above, FELIX provides several functions for automatic phasing of a 1D spectrum. To use one of these methods, select the Automatic option in the Process1D/Phase Correction command, then select one of the four Auto Method options.

The automatic phasing methods include:

Except for the basic method, you can specify one or more excluded areas, to exclude solvent peaks when calculating the phase parameters. For the PAMPAS and APSL methods, you can also specify a Filter Width, which is the minimum peak width (at the peak bottom) required for a sample peak to be used in the calculation of phase parameters.

FELIX selects the default values for Auto Method and Filter Width automatically, based on the spectrum data in the workspace. However, you can change these settings.


Process1D/Baseline Correction

The Process1D/Baseline Correction (<Alt>+sb) command contains options that deal with baseline points or do baseline correction.

Auto Pick Points

To define baseline points, select the Auto Pick Points option in the Process1D/Baseline Correction command. FELIX generates a list of baseline points. Display markers for each baseline point picked in the spectrum are shown at the bottom of the current spectrum.

Auto Pick Points w/FLATT

The Auto Pick Points w/FLATT option of the Process1D/Baseline Correction command uses the FLATT algorithm (Guntert 1992) for selecting baseline points in a spectrum. The resulting points are stored in the entity whose name is stored in the symbol basent.

FELIX first prompts you to specify the Basepoint Line Width to use in calculating the chi value for the spectrum. Next, FELIX prompts you to specify the Baseline Width, Minimum Chi Square, Factor(tau), and Stride to use in selecting the baseline points. For a more complete description of the required parameters, please see the abp and chi commands in Appendix A of the FELIX Command Language Reference manual.

Pick Points via Cursor and Manual Pick Points

To add baseline points singly, use the Pick Points via Cursor option or the Manual Pick Points option of the Process1D/Baseline Correction command. Select each baseline point via a cursor; or, type in the desired points via a menu interface. To use the cursor, add points by clicking the desired baseline points with the crosshair cursor. To exit this mode, click outside the spectrum.

Delete All Points

To delete all the baseline points, select Delete All Points in the Process1D/Baseline Correction command. FELIX deletes the current baseline points entity from the database; FELIX prompts you to confirm this action via a dialog box.

Delete Points in Region

If you make a mistake while selecting individual baseline points or if you want to modify the current list of baseline points, you may delete a region of points using the graphical interface. First, select Delete Points in Region in the Process1D/Baseline Correction command to create a small crosshair cursor. Then drag out a region of baseline points to delete.

Baseline correction

Once the baseline points are defined, you can choose one of several baseline-correction algorithms:

The baseline-correction algorithm generates smoother baseline correction functions from baseline points. The Polynomial correction option of the Process1D/Baseline Correction command differs from the cubic spline correction algorithm in that the baseline does not necessarily pass exactly through each baseline point, but a best fit is calculated. In addition, you may set the order of the polynomial (from 2 to 9) in the polynomial control panel. A polynomial of order two yields a smooth parabolic function, and a polynomial of order nine generates a more complex correction function. A polynomial of an order between three and five is usually sufficient to give accurate baseline correction.

Use the FELIX real-time baseline-correction feature to adjust the coefficients of a polynomial baseline function while displaying both the resulting baseline function and baseline-corrected spectrum superimposed.

When you select the Real-Time Polynomial option of the Process1D/Baseline Correction command, FELIX prompts you to specify a polynomial order for the correction function and an interval width; this is used to average baseline point values as described earlier.

Click OK, and FELIX displays the real-time baseline correction interface. When you finish correcting the baseline you can exit the interface and keep the corrected spectrum (Keep) or Cancel the interface and restore the original spectrum.

To alter the displayed region along the x axis of the spectrum, click xpand and using the small crosshair cursor to drag a box around the desired region. To restore the complete spectrum, click Full. If you are dissatisfied with any of the baseline points, which are indicated by red ticks below the spectrum, add or remove points by clicking Add Points or Delete Points. When you are satisfied with the baseline points, click Fit to automatically calculate the polynomial coefficients (the calculated baseline appears as a red line superimposed on the spectrum) and click Apply to apply the correction to the spectrum.

Use the slider located along the bottom of the interface to adjust the polynomial coefficients individually in real time. First, select the individual coefficient through the popup next to the slider. Again, when the red baseline appears to coincide with the spectrum baseline, click Apply to correct the spectrum. You can zero the polynomial coefficients by clicking Zero and restore the original spectrum by clicking the Reset button. In addition, the displayed spectrum can be shifted and stretched vertically with the keypad.

The cubic spline algorithm, applied by selecting the Cubic Spline option from the Process1D/Baseline Correction command, generates a baseline that passes exactly through each baseline point. A cubic spline may yield a kinked baseline if the defined baseline data points are close together and noisy. To minimize this problem, adjust the interval width reserved symbol iwidth to a number larger than 1. Increasing the interval width minimizes the kinked baseline problem by averaging the data values in an interval of points around each picked point and using that average value as the baseline point.

To use a baseline-correction function supported by FELIX that does not require explicit baseline points, select the Automatic w/ABL option from the Process1D/Baseline Correction command. FELIX selects noise points and performs a baseline correction for each point. You must input values for the noise level and the peak size in points.

Note: Depending on the number of points in your spectrum and your line widths, these values may need to be adjusted several times to fit your data. Therefore, you should save a nonbaseline-corrected spectrum before applying the correction. This algorithm was reported by Dietrich et al. (1991) and implemented by W. Massefski.

FELIX also provides the FLATT baseline-correction algorithm, a technique introduced by Guntert and Wuthrich (1992). The FLATT algorithm locates baseline segments in the spectrum and uses linear least-squares to fit a truncated Fourier series to these points.

To use FLATT, select the Automatic w/FLATT option in the Process1D/Baseline Correction command. FELIX prompts you to specify the Basepoint Line Width, which is used to calculated the minimum chi-square value. Enter an integer with a value that is small but larger than half the width of the widest peak.

When you click OK, FELIX determines a value for the minimum chi square, which should correspond to the contribution of noise to the chi-square value. FELIX displays this value in the next control panel, which opens automatically and prompts you to specify baseline-correction parameters. You must enter a value for the Baseline Width as you did for the minimum chi-square estimate. You may adjust the Minimum Chi Square value if you want.

The control panel also prompts you to specify the Points to Correct, which is the number of Fourier series terms used to fit the baseline, and the Factor (Tau), which specifies how much larger than the minimum chi-square value a segment's chi-square value can be and still be considered baseline. When the chi-square value of a segment exceeds the product of the minimum chi-square value and the Factor (Tau), the segment is considered to contain peak information and is rejected as baseline. To perform this action, click OK.

FELIX also provides the FaceLift baseline-correction algorithm (Chylla & Markley 1993). This signal-recognition based utility identifies baseline points and subtracts the baseline points from the original spectrum data.

To use FaceLift, select the Automatic w/FaceLift option in the Process1D/Baseline Correction command. FELIX prompts you to specify the Filter Width, which is the half-width of the smoothing data window over which datapoints are sampled. The half-width determines the minimum line width of artifacts that will be removed from the spectrum. The recommended range is 32-64 datapoints (powers of 2 are not necessary). Use the Number of Standard Deviations to determine a threshold standard deviation, above which any point is considered to be a signal point. The recommended range is 2.5-3.0. Click OK to execute the FaceLift algorithm.


Process1D/Open Process

Use the Process1D/Open Process command (<Alt>+s1) to interactively process 1D data or the first FID of an ND data set.

First, FELIX displays a control panel where you can specify the Filter Type for the kind of data you want to process. In general, if you are working with raw spectrometer data, you should specify All Files (BRUKER, VARIAN, JEOL:*) as the Filter Type.You can then navigate through the desired directories to get to the data.

At this point you want to select the actual spectrometer datafile. This is usually an FID or SER file. To select the FID double-click the filename; or, click the filename and then click OK.

When you click OK, FELIX displays a control panel containing the 1D header menu parameters, which are taken from the header information of the spectrometer datafile.

Be sure to check that the proper parameter values are displayed and correct them if necessary. If the Data Type parameter is Complex, the Data Size parameter is in complex points. Spectrometer data generally have a Data Type of Complex. The Bruker Data Type is used only for Bruker QSEQ data where data points are collected alternately as on some older Bruker spectrometers.

When you are satisfied that the header parameters are correct, click OK.

FELIX now displays the main 1D data-processing control panel, whose controls are grouped into several sections. The top section lists the individual processing options. These options are similar to those used for 2D/3D/4D data processing. See Table 19 for more information on the individual processing options.

The Interactive Processing section of this control panel contains a set of controls for interactively processing the data while varying the parameters for a specific processing action. The bottom section of the control panel specifies the manner in which the processing is done. Click Apply to perform the operations specified in the list of processing operations and redisplay the main processing panel. click OK to perform the indicated processing options and close the panel.

Note: To use this control panel, it is a good idea to set up the basic processing first. For example, try setting FT, Set Phase Correct, and Real Time to on. Then click Apply. This performs the FT operation and starts the real-time phase interface. At this point you can adjust the phase interactively. When you finish phasing (click Keep in the phase panel) you are brought back to the main 1D processing control panel, where you can select other specific processing options. Here it is often a good idea to set the Phase Correct mode to Use Current. The current phasing parameters are then used for subsequent phasing operations.

To interactively vary the parameters for the chosen processing step, click one of the Interactive Processing buttons. The Interactive Processing options allow you to control the various processing parameters with sliders. As you adjust the sliders you can simultaneously see the effect on the FID. These interactive options also allow you to display the transformed spectrum. This way you can see the effect of varying a processing parameter on both the FID and the transformed spectrum. Click Keep in one of these interactive processing panels to return to the main control panel. To exit the main processing panel, click OK or Cancel.


ProcessND pulldown


ProcessND/Open and Process 2D

Use the ProcessND/Open and Process 2D command (<Alt>+s2) process 2D data. FELIX displays a control panel to specify the Filter Type for the kind of data you want to process. In general, if this is the initial processing of raw spectrometer data set you should specify All Files (Bruker, Varian, Jeol:*) as the Filter Type. You can then navigate through the desired directories to get to the data. You must select the actual spectrometer datafile, which is usually an FID or SER file. To select the FID double-click the filename, or select the filename and then click OK.

FELIX next displays a control panel with the 2D header menu parameters. These parameters are taken from the header information of the spectrometer datafile. Be certain that the proper parameter values are displayed and correct them if necessary. Then set the Data Source to correspond to the type of data you have. The choices are: General, Bruker, Varian, and Jeol. Use the Data Source setting to determine how to enter the acquisition information in relationship to how the data were collected.

General Processing

If you set the Data Source to General, FELIX displays a general control panel for processing 2D data that are not related to any specific spectrometer type. If you select General or Jeol processing, you are presented with the same control panel of generalized processing choices. The Data Type parameter relates to the form of the FID in the D1 (t2) dimension. The FID in the acquisition dimension is almost always Complex.

When FELIX processes 2D data, the method used to collect the data in the indirectly detected dimension affects how the data are processed in the acquisition dimension. This simplifies data processing in the indirect dimension and makes it easier to examine the data along this dimension.

The indirect dimension is almost always processed as States or TPPI. Thus, for the Acquisition Mode, this parameter determines how the D1 (t2) dimension is processed, but is set based on how the indirectly detected dimension was collected. So if data were collected as a Bruker style echo/anti-echo experiment in D2 (t1), the Acquisition Mode is set to Echo/Anti-Echo and the Acquisition in D2 parameter is set to States. This is because the Echo/Anti-Echo experiment results in a complex interferogram along t1.

Bruker Processing

If you are processing Bruker data, it is generally easier to set the Data Source parameter to Bruker. FELIX displays a simplified control panel specifically for Bruker data. The Data Type parameter is Complex unless you have an FID where the data points are sampled sequentially. The Acquisition in D2 parameter is set based on the Bruker mode of data collection. You can generally determine this from the value of the MC2 parameter in the Bruker proc2s parameter file.

Varian Processing

If you are processing Varian data it is generally easier to set the Data Source parameter to Varian. FELIX displays a simplified control panel specifically for Varian data. The Data Type parameter is Complex. The Acquisition Mode parameter is set based on the type of experiment you have. Varian data is most often collected as States. If you have a sensitivity-enhanced sequence of the Lewis Kay type, set Acquisition Mode to Sensitivity Enhanced. If you use the grad_sort_nd program to pre-process your data before processing on the Varian, then your data is of the Sensitivity Enhanced Type.

After you specify the acquisition parameters, click OK. FELIX displays the main 2D control panel. Here you specify the exact sequence of options to use during processing. See Table 20 for more information on the various processing options. When you click OK from this control panel FELIX prompts you to supply any needed additional information, and then processing is performed. When you process the D1 dimension of a 2D data set the matrix is first built and then the individual vectors from the input data set are read in, processed, and stored in the matrix.

To process the second dimension of a 2D data set, select the ProcessND/Open and Process 2D command again and specify a file type of FELIX Matrix. In the header menu verify that the Data Source parameter is still correct. Then select the D2 dimension for processing in the main 2D control panel. When you click OK, the individual vectors from the matrix are read in one at a time, processed, and stored in the matrix.


ProcessND/Open and Process 3D

Use the ProcessND/Open and Process 3D command (<Alt>+s3) to process 3D data. FELIX displays a control panel where you can specify the Filter Type for the kind of data you want to process. In general, if this is the initial processing of raw spectrometer data, you should specify All Files (Bruker, Varian, Jeol:*) for the Filter Type. You can then navigate through the desired directories to get to the data. You must select the actual spectrometer datafile. This is usually an FID or SER file. To select the FID, double-click the filename or select the filename and then click OK.

At this point FELIX displays the 3D header menu parameters. These parameters are taken from the header information of the spectrometer datafile. Verify that the proper parameter values are displayed and correct them if necessary. Set the Data Source to correspond to the type of data you have. The choices are General, Bruker, Varian, and Jeol. The setting for Data Source determines how you enter the acquisition information in relationship to how the data were collected.

General Processing

If you select General as the Data Source FELIX displays a general control panel for processing 3D data that are not related to any specific spectrometer type. Selecting General or Jeol processing opens the same control panel of generalized processing choices. The Data Type parameter relates to the form of the FID in the D1 (t3) dimension. The fid in the acquisition dimension is almost always Complex.

When you process 3D data in FELIX, the method used to collect the data in the indirectly detected dimensions also affects how the data are processed in the acquisition dimension. This simplifies data processing in the indirect dimensions and makes it easier to examine the data along these dimensions.

The indirect dimensions are almost always actually processed as States or TPPI. Thus for the Acquisition Mode this parameter determines how the D1 (t3) dimension is processed but is set based on how the indirectly detected dimensions were collected. So if the data were collected as a Bruker style echo/anti-echo experiment in D3 (t1) and states-TPPI in D2(t2), then Acquisition Mode is set to Echo/Anti-Echo States-TPPI and the Acquisition in D2 and Acquisition in D3 parameters are both set to States. This is because the echo/anti-echo experiment results in a complex interferogram along t1.

The Acquisition Method determines how the t1-t2 time point values are collected. If the data are collected as a group of four complex FID's corresponding to each t1-t2 time point, then the Acquisition Method is Quartets. If the data are collected, for example, as pairs of real and imaginary t2 components for all of the real t1 values, followed by the series of pairs for the imaginary t1 values, then this is referred to as Planes. Bruker generally collects data as planes, while Varian generally collects data as quartets.

The First Incremented parameter specifies the order in which the FID's were collected. If First Incremented is set to t2, this means that the t2 parameter was incremented first and then the t1 parameter; that is, for each t1 time increment the entire set of t2 time increments is collected before proceeding to the next t1 time value.

Quartet Order Parameter

Use the Quartet Order parameter when the Acquisition Type has been set to Quartets. It determines the order in which the individual elements of the complex quartet are collected and therefore which dimension in the quartet is incremented first.

If the Quartet Order parameter is set to t2, this implies that the FID's were collected in the following sequence:

FID# t1(D3) t2(D2)
1

real

real

2

real

imaginary

3

imaginary

real

4

imaginary

imaginary

If the Quartet Order parameter is set to t1, this implies that the FID's were collected in the following sequence:

FID# t1(D3) t2(D2)
1

real

real

2

imaginary

real

3

real

imaginary

4

imaginary

imaginary

Bruker Processing

If you are processing Bruker data it is generally easier to set the Data Source parameter to Bruker. FELIX displays a control panel specifically for Bruker data. The Data Type parameter is Complex unless you have an FID in which the data points are sampled sequentially. The Acquisition in D2 and Acquisition in D3 parameters are set based on the Bruker mode of data collection. You can generally determine this from the values of the MC2 parameters in the Bruker proc2s and proc3s parameter files.

The Acquisition Order parameter is determined by which dimension (t1 or t2) is incremented first. If t1 is incremented first, then the Acquisition Order is set to "3-1-2". If t2 is incremented first then it is set to "3-2-1".

Varian Processing

If you are processing Varian data it is generally easiest to set the Data Source parameter to Varian. FELIX displays a control panel specifically for Varian data. The Data Type parameter should be set to Complex. The Acquisition Mode parameter is set based on the type of experiment. Varian data are most often collected as States. If you have a sensitivity-enhanced sequence of the Lewis Kay type, then set the Acquisition Mode parameter to Sensitivity Enhanced. If your data were pre-processed using the grad_sort_nd program before processing on the Varian, then your data are of the Sensitivity Enhanced Type.

Set the First Incremented parameter based on which dimension is incremented first. Varian data are most often collected as "d3, d2". Set the Quartet Order parameter based on the order in which the elements of the complex quartet of FID's were collected. This parameter is set based on the array parameter in the Varian procpar file. Set this parameter to phase, phase2, or phase2, phase, depending on the value of the array parameter.

After you specify the acquisition parameters, click OK. FELIX displays the main 3D processing control panel. Here you specify the exact sequence of options that will be used during processing. See Table 20 for more information on the various processing options. When you click OK in this control panel, FELIX prompts you to supply any needed additional information and then processing is performed. When you process the D1 dimension of a 3D data set the matrix is first built and then the individual vectors from the input data set are read in, processed, and stored in the matrix.

To process the second dimension of a 3D data set, select the ProcessND/Open and Process 3D command again. Now specify a file type of FELIX Matrix. In the header menu, be sure that the Data Source parameter is still correct. Then in the main 3D processing control panel, select the D2 dimension for processing. When you click OK, the individual vectors from the matrix are read in one at a time, processed, and stored in the matrix.


ProcessND/Open and Plane Process 3D

Use the ProcessND/Open and Plane Process 3D command (<Alt>+sl) to process a 2D plane from a 3D data set. This command is similar to the ProcessND/Open and Process 3D command described above. The difference is that plane processing creates a 2D matrix instead of a 3D matrix. This function builds the 2D matrix, reads in each vector from the input data set, processes them, and stores them in the 2D matrix. After performing this step, you will have a 2D matrix that is processed in the D1 dimension only. You must then use the ProcessND/Open and Process 2D command to process the D2 dimension of this new matrix.

In the control panel for processing parameters you can specify a D1-D2 (t3-t2) plane or a D1-D3 (t3-t1) plane for processing. The other options in the various panels are the same as for 3D processing, described above.


ProcessND/Open and Process 4D

Use the ProcessND/Open and Process 4D command (<Alt>+s4) to process 4D data. FELIX displays a control panel to specify the Filter Type for the kind of data you want to process. In general if this is the initial processing of a raw spectrometer data set, you should specify All Files (Bruker, Varian, Jeol:*) as the Filter Type. You can then navigate through the desired directories to get to the data. Select the actual spectrometer datafile. This is usually an FID or SER file. To select the FID double-click the filename, or select the filename and then click OK.

Next FELIX displays the 4D header menu parameters. These parameters are taken from the header information in the spectrometer datafile. Verify that the proper parameter values are displayed and correct them if required. Set the Data Source parameter to correspond to the type of data you have. The choices are Unknown, Bruker, Varian, and Jeol. 4D data are handled with a general processing scheme that is not specific to any spectrometer type. The acquisition parameters to be entered for 4D data are analogous to those for 3D data with an additional dimension. For more information on entering the acquisition information see "General Processing". The processing options are the same as those for 2D and 3D data.


ProcessND/Phase Correct

Processed data occasionally require re-phasing in one or more dimensions. Use the ProcessND/Phase Correct (<Alt>+ph) command to re-phase a previously processed ND dataset that is currently open in the frame. FELIX displays a control panel to specify the dimension to rephase and the method. In addition to automatic phasing, you can give explicit values for the phasing parameters Phase0 and Phase1 or adjust the phase parameters interactively. click OK to re-phase all vectors in the matrix using these phase parameters (the matrix must be write-enabled).

If you select the automatic phasing function, you can select PAMPAS or APSL as the phase-detection algorithm and can define some excluded areas, to exclude noise while searching the sample peaks for calculation of phase parameters. You can also specify a Filter Width, which is the minimum peak width (at the peak bottom) required for sample peaks. FELIX suggests a value for Filter Width based on the matrix data, but you can change the value.


ProcessND/Baseline Correct

FELIX provides a host of baseline-correction options, and three of the more popular methods, FLT, convolution, and FaceLift, have been used as the basis for a set of post-transform baseline-correction commands. All the available baseline-correction methods are discussed in detail under "Process1D/Baseline Correction". Use the ProcessND/Baseline Correct command (<Alt>+pb), to specify the method and which dimension the baseline correction should proceed along.

FLATT method

The FLATT command conducts baseline correction on the selected dimension of the transformed ND data using the algorithm of Guntert and Wuthrich (1992). The FLATT algorithm discriminates baseline segments and uses a linear least-squares solution to fit a trigonometric series to the baseline points.

Use Baseline width to determine a minimum chi-square value. A value that represents the half-width (in points) of the broadest resonance in the spectrum generally yields satisfactory results.

Use Points to Correct to specify the number of trigonometric terms to use in the baseline fit. Use Tau to specify the factor by which a segment may exceed the minimum chi-square value and still be considered a baseline segment. You may directly specify the source of the chi-square value or allow the utility to derive it (the value then represents the average over all vectors in the matrix). Armed with these values, the function loads and baseline-corrects every vector in the matrix (the matrix must be write-enabled).

Convolution method

Use the Convolution command to conduct baseline correction on the selected dimension of transformed ND data using the algorithm of Dietrich et al. (1991) as developed by W. Massefski. This ABL-based utility automatically discriminates baseline segments and conducts a running-average convolution of the baseline points, while a simple linear correction is applied to the intervening spectrum regions.

Use Noise size to specify the convolution width (in points) for the baseline regions. Peak size represents the half-width (in points) of the broadest resonance in the spectrum. Using these values, the function loads and baseline-corrects every vector in the matrix (the matrix must be write-enabled).

FaceLift method

Use the FaceLift function to conduct baseline correction on the selected dimension of transformed ND data using the algorithm of Chylla and Markley (1993). This signal recognition-based utility identifies baseline points and filters the high-frequency noise along other dimensions before the baseline matrix is subtracted from the original matrix.

Use Filter Width to determine the half-width of the smoothing data window over which datapoints are sampled. The recommended range is 32-64 data points (powers of 2 are not necessary).

Use Number of Standard Deviations to determine a threshold standard deviation, above which any point is considered to be a signal point. The recommended range is 2.5-3.0.

Use D1 (D2, D3, or D4) Points to Smooth to calculate the half-width of the smoothing data window that is used to smooth the base-point correction matrix along D1 (D2, D3, or D4). If it is the same dimension as that being baseline corrected, you should use the same value as for the Filter Width. Otherwise, a value of 2-4 is recommended (the matrix must be write-enabled).


ProcessND/Reverse Matrix

Certain hypercomplex phase-cycling protocols effectively render the complex-conjugate of what is normally expected by the ND States processing utility. Such data appear to be reversed in the D2 and/or D3 and/or D4 dimension. If prior experience indicates that such a situation prevails for your data, you may specify that data vectors be reversed in D2 and/or D3 and/or D4 as a part of the ND processing.

Use the ProcessND/Reverse Matrix (<Alt>+pr) command to specify the dimension to reverse in the currently open matrix. Every vector along the specified dimension is reversed (the matrix must be write-enabled).


ProcessND/Utilities

Squeeze Matrix

Use the ProcessND/Utilities/Squeeze Matrix (<Alt>+pss) command to squeeze the current matrix (that is, to discard all the points below the threshold you define). This is useful for retaining only those portions of the matrix where real peaks can be found. Depending on the threshold, you can compress the file quite a bit, which can speed up the redraw and shorten the access time for originally large 3D and 4D spectra.

Note: This procedure is irreversible, and some actions (for example, volume measurement and peak optimization) may not work well on such a matrix.

Unsqueeze Matrix

Use the ProcessND/Utilities/Unsqueeze Matrix (<Alt>+psu) command to create an unsqueezed matrix from a previously squeezed one. This command is not the reverse of ProcessND/Utilities/Squeeze Matrix, since it merely inserts zeros in those places in the matrix that were previously (during a squeeze) discarded.

Transpose Matrix

Use the ProcessND/Utilities/Transpose Matrix (<Alt>+pst) command to swap two dimensions of a processed matrix.

Projection

Use the ProcessND/Utilities/Projection (<Alt>+psp) command you to create a 2D projection of the current 3D or 4D matrix.

Diagonal Plane

Use the ProcessND/Utilities/Diagonal Plane (<Alt>+psd) command to extract a 2D diagonal plane from a typically homonuclear 3D matrix.


Tools pulldown

FELIX includes several menu items (commands) that affect frequency-domain spectra in the workspace. Most of these functions are directly related to the transformation of multi-dimensional spectra, but several affect the processing of 1D data.


Tools/Buffers

Buffers are accessed from within the interface by selecting the Tools/Buffers command (<Alt>+tb).

Store Work to Buffer

To store the current information in the workspace to a buffer, select the Tools/Buffers/Store Work to Buffer command (<Alt>+tbs) and enter the buffer number in the control panel. To visualize this information, you must change the stack depth to include that buffer. This action is useful for saving a spectrum when the workspace is needed for some other process.

Load Work from Buffer

To load buffer information to the workspace, select the Tools/Buffers/Load Work from Buffer command (<Alt>+tbl) and enter the buffer number.

Add Work to Buffer

Use the Tools/Buffers/Add Work to Buffer command (<Alt>+tba) to add the current contents of the workspace to the specified buffer. This action is especially useful for generating projections of multi-dimensional spectra and for co-adding the absorptive components of hypercomplex data.

Multiply Work by Buffer

Use the Tools/Buffers/Multiply Work by Buffer command (<Alt>-tbm) to multiply the data in the workspace by the contents of the defined buffer. This action is most often used to multiply the data in the workspace by an apodization function that was stored earlier in a buffer.

Subtract Work from Buffer

Use the Tools/Buffers/Subtract Work from Buffer command (<Alt>-tbu) to subtract the contents of the workspace from the defined buffer. This action is especially useful for generating projections of multi-dimensional spectra and for co-adding the absorptive components of hypercomplex data.

Push Work to Stack Top

Use the Tools/Buffers/Push Work to Stack Top command (<Alt>+tbp) to push data into the buffers. FELIX stores the contents of the workspace on the top of the buffer stack. Every time you push onto the stack, you increase the stack depth by one.

Pop Work from Stack Top

Use the Tools/Buffers/Pop Work from Stack Top command (<Alt>+tbt) to load the contents of the top of the buffer stack to the workspace and decrease the stack depth by one. Use this command in conjunction with the Tools/Buffers/Push Work to Stack Top command, t.

Exchange Work/Stack Top

Use the Tools/Buffers/Exchange Work/Stack Top command (<Alt>-tbx) to exchange the contents of current workspace with the top of the buffer stack. This is useful for moving data back and forth between workspace and the buffers.

Zero Stack Depth

Use the Tools/Buffers/Zero Stack Depth command (<Alt>+tbz) to reset the stack display to show only the current workspace. This option is useful to bring the program back to a pre-defined state.


Tools/Lists

One of the most important features of the FELIX database facility is the ability to create fast read-only representations of database entities, or lists. Such lists do not actually hold database information per se, but consist of pointers to items in a database entity. Lists exist in the memory that is allocated to the 1D buffers, so extremely long lists may require memory reconfiguration.

The Tools/Lists (<Alt>+tl) command displays a pullright sub-menu of items, as described below.

List 1...4

Use the Tools/Lists/List 1...4 (<Alt>+tl1...4) command to select from among four lists. All subsequent Lists commands then operate on the selected list, which is symbolized by the pushed-in toggle button beside it. When you change the list number, cross-peak footprints referenced by that list are not automatically drawn.

Draw

Use the Tools/Lists/Draw (<Alt>+tld) command to display the contents of the current list, using the color specified for that list.

Color

Use the Tools/Lists/Color (<Alt>+tlc) command to specify a footprint color for each of the four lists. The default pen color aliases are listed in Table 7.

Zero

Use the Tools/Lists/Zero (<Alt>+tlz) command to re-initialize (or zero) the current list.


List contents

Lists are composed using any of the six commands in the next group. The actions of all these commands are cumulative, so you can use them to compile complex sets of cross peaks into one list.

Select Displayed

Use the Tools/Lists/Select Displayed (<Alt>+tlp) command to add all footprints in the currently displayed region to the current list.

Select Region

Use the Tools/Lists/Select Region (<Alt>+tlr) command to add only the footprints in the interactively defined region to the current list.

Select Line

Use the Tools/Lists/Select Line (<Alt>+tli) command to add footprints which intersect any part of the displayed cursor to the current list.

Find by Name

If the cross peak entity contains assigned peaks, then use the Tools/Lists/Find by Name (<Alt>+tln) command to create lists using peak names (using either partial or complete names).

Add One, /Remove One

Interactively add or remove footprints from the current list using the Tools/Lists/Add One (<Alt>+tla) and Tools/Lists/Remove One (<Alt>+tlo) commands.


List action

Lists may be organized and reviewed using any of the four commands in the next category.

Merge Lists

Use the Tools/Lists/Merge Lists (<Alt>+tlm) command to derive a third list from the union or the intersection of two other lists.

Sort

Use the Tools/Lists/Sort (<Alt>+tls) command to sort lists in ascending or descending order, according to the D1-center or D2-center fields in the cross-peak entity.

View

Use the Tools/Lists/View (<Alt>+tlv) command to review items that are referenced in the current list. FELIX displays a control panel where you specify whether to display peak centers, widths, and names using data points or ppm units. This displays a spreadsheet of cross peaks, which should not be edited.

Write

Use the Tools/Lists/Write (<Alt>+tlw) command to create a hardcopy of the items that are referenced in the current list. FELIX displays a control panel to specify whether to display peak centers, widths, and names using data points or ppm units. These written lists are for record-keeping only and cannot be read back into FELIX.


Tools/Generate Spectrum/FID

Use the Tools/Generate Spectrum/FID command (<Alt>+ts) to simulate spectra, FIDs, and noise.

Use the Spectrum from Parameters option to generate single spectrum lines from an amplitude, frequency, and line widths. You can generate Lorentzian, Gaussian, and Voigt line shapes. The spectrum line can overwrite the workspace or be added to the workspace.

Use the FID from Parameters option to generate a free induction decay (FID) from an amplitude, frequency, and a time constant. FIDs can overwrite the workspace or be added to the workspace.

Use the Add Noise option to generate white noise. The noise can overwrite the workspace or be added to the workspace.

The Spectrum from File option generates a 1D theoretical spectrum from a TurboNMR NMR shielding output file.

The Spectrum from Peaks option generates a 1D theoretical spectrum from a 1D peak entity in the database.


Tools/Functions

The Tools/Functions command (<Alt>+tf) displays a pullright sub-menu of items for dealing with the workspace and defining specific data values within the workspace.

Reduce to Real

Use the Tools/Functions/Reduce to Real command (<Alt>+tfr) to convert a complex spectrum to a real spectrum by discarding the imaginary part of the data in the workspace.

Complex

Use the Tools/Functions/Complex command (<Alt>+tfc) to convert a real spectrum into a complex spectrum with a zeroed imaginary part.

Reverse

Use the Tools/Functions/Reverse command (<Alt>+tfv) to reverse the data in the workspace by swapping datapoint values. Thus, data point 1 is swapped with data point N, and data point 2 is swapped with data point N-1, etc.

Complex Conjugate

Use the Tools/Functions/Complex Conjugate command (<Alt>+tfo) to negate the imaginary part of the data in the workspace. This action reverses a spectrum if it is performed before executing a Fourier transform.

Magnitude Spectrum

Use the Tools/Functions/Magnitude Spectrum command (<Alt>+tfm) to replace the real part of the workspace with the square root of [(real)2+(imag)2], or the absolute magnitude of the data, and to replace the imaginary part of the workspace with the arctan (real/imag) or the phase array of the data, in the range -180 to +180.

Power Spectrum

Use the Tools/Functions/Power Spectrum command (<Alt>+tfp) to replace the real part of the data in the workspace with [(real)2+(imag)2], or the power spectra, and to set the imaginary part of the data to zero.

Alternate Real/Imaginary

Use the Tools/Functions/Alternate Real/Imaginary command (<Alt>-tfa) to change a spectrum that has been separated into real and imaginary parts into alternating real and imaginary parts. Alternating is the standard order where the real and imaginary parts of each data point are adjacent.

Separate Real/Imaginary

Use the Tools/Functions/Separate Real/Imaginary command (<Alt>-tfs) to convert a spectrum that is in standard order into separate real and imaginary parts. In separate order, the real parts of all datapoints come first, followed by the imaginary parts of all datapoints.

Exchange Real/Imaginary

Use the Tools/Functions/Exchange Real/Imaginary command (<Alt>-tfe) to exchange the real and the imaginary parts of the workspace. This action is most often used when you need to add the real component of a FID (that is, the part of the real serial file) to the real component of a FID that is part of the imaginary serial file.

Shift Data

Use the Tools/Functions/Shift Data pullright (Alt-tfd) commands to shift the data in the workspace a specified number of points to the left or right.

Set Data Size

The Tools/Functions/Set Data Size command (<Alt>+tfi) provides options to alter the size or number of datapoints in the workspace.

Fold Data

The Tools/Functions/Fold Data command (<Alt>+tff) provides options for folding and unfolding data in the workspace.


Tools/Mathematics

Set Data

The Tools/Mathematics/Set Data (<Alt>+tms) command includes three options:

Zero Data

The Tools/Mathematics/Zero Data (<Alt>+tmz) command contains several options for zeroing various datapoints in a spectrum:

Multiply Data

Use the Tools/Mathematics/Multiply Data command (<Alt>+tmm) to multiply all points in the workspace by a number. If the data in the workspace are complex, then the multiplier may be complex. Use this action to change both the magnitude and phase of the data in the workspace.

Add To Data

Use the Tools/Mathematics/Add To Data command (<Alt>+tma) to add a number to all points in the workspace. The number may be real or complex.

Absolute Value of Data

Use the Tools/Mathematics/Absolute Value of Data command (<Alt>-tmv) to replace each point in the workspace with its absolute value.

Inverse of Data

Use the Tools/Mathematics/Inverse of Data command (<Alt>+tmi) to replace the data in the workspace vector with its inverse. This action takes the reciprocal of each point in the workspace (replace value by 1/value) and stores the new value in the workspace. Any zero points in the workspace are skipped to avoid a divide-by-zero error. Use this action to create novel and interesting window functions for apodization.

Logarithm of Data

Use the Tools/Mathematics/Logarithm of Data command (<Alt>+tml) to replace each datapoint in the workspace with its natural (base e) logarithm. Use this action to compute some novel window function for apodization. Any zero points in the workspace are skipped to avoid a divide-by-zero error.

Anti-Logarithm of Data

Use the Tools/Mathematics/Anti-Logarithm of Data command (<Alt>+tmn)to replace each data value in the workspace with exp(value), its natural (base e) anti-logarithm or exponential.

Derivative of Data

Use the Tools/Mathematics/Derivative of Data (<Alt>+tmd) to push the derivative of the data in the workspace onto the current buffer stack.

Integral of Data

Use the Tools/Mathematics/Logarithm of Data command (<Alt>+tmt) to push the integral of the data in the workspace onto the current buffer stack.


Peaks pulldown

Pick 1D or ND peaks or resonances with the items in the Peaks pulldown (<Alt>+k). The commands in this pulldown work differently, depending on whether the active frame contains a 1D spectrum or an ND matrix.


Peaks/Pick One

Use the Peaks/Pick One command (<Alt>+ka) to select one peak at a time. To change the pick parameters, select Preference/Pick Parameters.


Peaks/Pick Region

To select peaks in a sub-region of your display, select the Peaks/Pick Region command (<Alt>+kg).

If you have a 1D spectrum or an ND spectrum for which the Pick Region Mode in the Preference/Pick Parameters control panel is set to Define by Cursor, FELIX displays a small crosshair cursor that you can use to drag out a region.

Otherwise for ND spectra, FELIX picks-peaks in the displayed region (Pick Region Mode was set to Displayed Region), or you can specify a region through a control panel (if Pick Region Mode was set to Define via Dialog).


Peaks/Pick All

Use the Peaks/Pick All command (<Alt>+kp) pick peaks in the full spectrum. FELIX displays a control panel where you can set the peak-pick parameters (which also can be accessed through the Preference/Pick Parameters command).


Peaks/Remove One

Use the Peaks/Remove One command (<Alt>+kn) to delete peaks one by one using the cursor.


Peaks/Remove Region

Use the Peaks/Remove Region command (<Alt>+kr) to delete peaks in a region that you select by dragging out with the small crosshair cursor.


Peaks/Remove All

Use the Peaks/Remove All command (<Alt>+kl) to delete the peak entity.


Peaks/Edit

Use the Peaks/Edit command (<Alt>+ke) to interactively move or adjust the cross-peak shape of a selected cross peak. First click on a cross peak to select it for editing. FELIX signals that the peak is selected by changing the cross peak's footprint color.

Next you have two choices: Adjust the footprint position by clicking near the center of the footprint and dragging, or adjust the cross-peak shape by clicking near the edge of the footprint and then dragging.

This function remains active until you press <Esc> key or click a point in the display at which no cross-peak footprint exists.


Peaks/Example Peak

For information on this command refer to "Preference/Pick Parameters" on page 134, in particular the information there for Stella Peak Picking.


Peaks/Filter

The Peaks/Filter (<Alt>+pf) command includes a set of tools for use after peak picking. These tools act as filters, eliminating a subset of cross peaks based on the criterion you select. Different numbers of tools are available, depending on the dimensionality of the spectrum.

Use the Remove Redundant Peaks command (<Alt>+kf) to remove redundant peaks for the set of picked 1D peaks.

Use the Remove Diagonal Peaks command to specify a filter tolerance (in datapoints, ppm, or Hz) and then remove cross-peak footprints that lie (within the specified tolerance) on the diagonal (D1=D2). For a 3D data set this diagonal can be any of the plane diagonals (D1=D2, D2=D3, or D1=D3) or the body diagonal (D1=D2=D3).

Use the Symmetrize Spectrum command to specify a filter tolerance (in datapoints, ppm, or Hz) and then remove cross-peak footprints that exist on only one side of the diagonal (that is, only those footprints at (D1,D2) which have symmetry-related partners at (D2,D1) are retained). This command also works for 3D spectra.

Use the Merge Multiplets command to specify a filter tolerance (in data points, ppm, or Hz) and then combine footprints that have D1/D2 centers within the specified tolerance of one another. The resulting footprints have widths that represent the largest of the widths of the unfiltered footprints in each dimension.

Use the Filter by Width command to specify a minimum and maximum footprint halfwidth (in datapoints, ppm, or Hz) and then remove footprints that fall outside the specified halfwidth limits.

Use the Filter by Volume command to specify a volume threshold and then removes peaks that have volumes below the specified threshold. Before you can use this command you need to measure the volumes.

Use the Filter by Intensity command to specify a lower and upper intensity threshold and then remove cross peaks that fall either outside or inside the limits.

Use the Remove Peaks in Region command to specify a region (in data points, ppm, or Hz) and then remove footprints that fall inside the specified limits.

Use the Remove Redundant Peaks command to remove footprints that have D1 and D2 centers at precisely the same position. The resulting footprints have widths that represent the largest of the widths of the unfiltered footprints in each dimension.

Use the Clean-up Ridges command to specify a strip width (in data points, ppm, or Hz) and the maximum number of peaks that there should be along each strip. The function then removes the excess low-intensity cross peaks in each strip. Use this action to clean up noise peaks when you know that, at a given frequency (within a certain tolerance), there cannot be more than a certain number of peaks (for example, in an HCCH-TOCSY spectrum along the aliphatic H dimension within 0.1 ppm in C and 0.02 ppm in H, there cannot be more than 10 peaks).

Use the Filter by Spectrum command to clean up the current spectrum. You can, for example, clean up a 3D HSQC-NOESY spectrum based on an HSQC spectrum. FELIX prompts you to specify a spectrum and peak table to use (usually a 2D HSQC spectrum). Then specify which dimensions from the 2D to use for accepting peaks in the current spectrum within the given tolerance. FELIX deletes all other peaks (most likely noise peaks).


Peaks/Optimize

This command (<Alt>+kz) offers a powerful line-fitting interface for deconvolution of complex spectra into individual peaks, which are described by an analytic function of intensity, linewidth, and frequency. These functions allow precise integration of individual peaks.

Depending on the dimensionality of the current spectrum, two different menu items can be accessed:

Select the Peaks/Optimize/Optimize command to access the 1D line-fitting command and other menu items that display the actual data, the synthetic data, and residual data,  either separately or all together in an overlay.

To fit a spectrum, first pick peaks using the Peak menu. this determines initial values for each peak's center, height, and width. Next select the Optimize command in the Peaks/Optimize menu. FELIX displays the interface in the current graphics frame with your spectrum in white, overlapped on the synthetic spectrum in red, and the synthetic line of a current peak in green. FELIX displays a modeless dialog containing buttons and sliders that permit you to fit the spectrum.

Note: Since this is a modeless dialog, use the main menu items to add or delete peaks. Thereafter, always press the Update Peaks button in the dialog so that the new peaks are accepted for optimization.

The buttons next to the Current Peak Item# let you select a current peak among the picked peaks to display its properties and a synthetic line in green. You can press Previous or Next to access different peaks, or click Cursor to select a peak with the mouse.

Integral shows the integral of the current peak. If needed, type in an arbitrary value and click the Normalize button to normalize the integral of all peaks relative to that value.

Use the slider and readouts in the right half of the control panel to modify the center, height, and width of the selected peak. As you adjust the slider, the synthetic spectrum and synthetic line are updated on the fly, so that you instantly see how your changes fit the real spectrum.

Before starting the automatic fitting, you can click the Setup button to activate another control panel where you can set certain initial parameters such as the Peak shape, which can be Lorentzian or Gaussian, and optimization locks, which prevent the automatic optimizer from adjusting the specified parameters.

In this control panel you can select the control parameters for simulated annealing function, and the length of the peak tails used to calculate the spectrum. Simulated annealing is always used as the optimization methods.

The peak tails are given as a percentage of the peak height. So, for example, a peak tails setting of 0.01 means that the peaks are calculated from their centers to the point where they fall to 1% of their maximum value. Use this setting to accelerate the optimization by avoiding needless calculation of the contribution of peaks in regions where they have little or no significant amplitude.

Click the Fit button to activate the automatic optimizer. During the optimization, FELIX updates the spectra in the display area to show the progress. If you want to abort the fitting before it's completed, press the <Esc> key.

Click OK to exit the curve-fitting dialog and accept the optimized peak parameters. The optimized peak data are stored in the existing 1D peak-picking entity. Or click Cancel to exit and ignore the changes.

Use Overlays to plot the actual, synthesized, and residual data at the same time.

Use Undo Overlays to remove the three data types mentioned above and displays only the actual data.

Use Actual Data to plot only the actual data.

Use Synthesize Data to plot the synthesized data only.

Use Residual Data to plot the residual data only.

Use Save Current Data to save the current spectrum to a 1D disk file.

ND peak optimization

Use this menu to optimize and model ND cross-peak footprints, shapes and volumes.

Note: All the menu items require that you already have an entity of picked peaks and an entity of measured volumes for at least one mixing time.

At the heart of these peak-optimization and -modeling functions is the notion of a model cross peak. Whereas an actual cross peak is described by a collection of adjacent data points in a matrix having intensities greater than the neighboring region, a cross-peak footprint is described by a set of center position and halfwidth values, and a volume is described as the total intensity of the cross peak's datapoints that lie inside the footprint; a model cross peak is defined as the distribution of intensity described by an idealized peak created from an analytic function of line widths, volume, and center positions.

FELIX uses either a Gaussian or Lorentzian line-shape function. The practical implication of these definitions is that FELIX can model the intensity of every cross peak that you have picked and measured a volume for, with a Gaussian or Lorentzian peak shape derived from the footprint and volume information.

The primary utility of these model cross peaks is twofold. First, you can display plots of model data or residual data (real minus model) to help with your early analysis and assignment work. There are many times when visually subtracting out a few well resolved peaks can reveal additional peaks hidden underneath. The second use for model cross peaks is to perform nonlinear least-squares optimizations on cross-peak shapes and intensities to yield the "best fit" values for peak center positions, halfwidths, and volumes; because the optimization algorithms seek to minimize the difference between the real data and the model representation of that data. Optimization can increase the confidence for assignment decisions based on peak alignment and improve volume buildup rate estimates for making distance restraints.

Use the Optimize command to execute a conjugate-gradient minimization algorithm (the quasi-Newton) to improve the values for peak centers, halfwidths, and/or volumes that are stored in the peak and volume entities. The algorithm used is the quasi-Newton, as mentioned in the 1D line-fitting section. FELIX displays a control panel that prompts you for a peak entity, a volume entity, a volume slot number, and the type of line shape to use. You may select which values to optimize and which values to hold constant.

Keep in mind that, for each peak, there are two (or three or four) centers, two (or three or four) widths, and one volume; and that all are fit against a rather small set of data points (the points inside that peak's footprint). Accordingly, the fewer the values that are optimized per peak, the better-determined the algorithm (and the faster it executes). You may find that optimizing just volumes, then just centers, and so on, gives better results than optimizing everything at once. Again, this is primarily a concern when there are relatively few datapoints per footprint.

Once you have selected which values to optimize, click OK. FELIX reports how many sets of peaks it will operate on and then announces each set optimized and colors those peaks in green as it completes each set. When all sets are done, FELIX reports the initial and final penalty values in the output window. These penalty units are on an arbitrary scale, yet they represent the RMS deviation in the intensity values at every datapoint in the optimized region of the matrix that has any cross peaks. Lower penalty values correspond to a better fit.

FELIX stores the new values for centers, halfwidths, and volumes in their respective entities.

Note: The results of this action cannot be undone, so you may want to save backup files of your peaks and volumes first.

Data modeling

So far we have only discussed the notion of actual matrix data. When you do a plot, the actual datapoints in the matrix are what get fed to the plot routine. In addition to actual data, FELIX can also display and analyze model and residual data.

Use the Actual Data command to use the actual matrix data. This reverses the actions of the Model Data and Residual Data commands.

Use the Model Data command to synthesize data from the current peaks and volumes, instead of reading datapoints from the matrix. All subsequent plots and analyses are performed on the synthesized model data. To return to using the actual matrix data, select the Peaks/Optimize/Actual Data command.

Use the Residual Data command to use a blend of real datapoints from the matrix and synthesized data from the current peaks and volumes. Specifically, the blend is "one part real minus one part model"; most commonly called the residual. All subsequent plots and analysis are performed on this residual data. Use this feature to measure the residual volume inside peak footprints that cannot be attributed to the peak, which is a sigma or uncertainty measurement for the real peak volume. To return to using the actual matrix data, select the Peaks/Optimize Peaks/Actual Data command.

Use the Model Parameters command to select whether Gaussian or Lorentzian line shapes are used in the modeling process.

Note: Be sure you remember to explicitly return to using actual data when you are finished investigating model and residual data.


Peaks/Brother Peak

Use the Peaks/Brother Peak command (<Alt>+kb) to explicitly extend assignments to other cross peaks along the D1 or D2 dimensions. You first select, with the crosshair cursor, a cross peak that already has assignments in one or more dimensions. You then explicitly select cross peaks that share the same D1 or D2 assignments.


Peaks/List

Use the Peaks/List (<Alt>+kl or <Ctrl>+l) command to check the status of individual peaks (chemical shifts, widths, peak assignments, and frequency assignments), which are listed in the output window or zoomed on in the peak table if it is open. You can click on a cross peak and the table scrolls to the location so that the row of that peak is visible and highlighted. Press <Esc> or click off a peak to exit.


Peaks/Find

Use the Peaks/Find (<Alt>+kd) command to find a specific cross peak. Search for a cross peak by its assignment name or its number. Or use the List/Name command to create a list of cross peaks that match a search criterion.

If you choose to search the cross-peak entity for a specified assignment name, or partial name, FELIX creates a list that contains the discovered peak(s). You may use a wildcard character (*) as part of the assignment name. If FELIX locates a peak, its display expands to show the found peak or the peak changes color, depending on your choice.


Peaks/Name One Peak

Use the Peaks/Name One Peak (<Alt>+ko) command to select a peak interactively and then assign names to the peak.


Measure pulldown


Measure/Cursor Position

The Measure pulldown includes functions for obtaining point numbers, ppm values, and corresponding data values. When you select the Measure/Cursor Position command (<Alt>+up) while a 1D spectrum is displayed, FELIX displays a vertical half-cursor. FELIX reports the current axis position and data value as you move the cursor. The axis position is in axis-based units . If your axis is in points, it tracks in points; if your axis is set to ppm, it tracks in ppm. To quit the cursor-tracking mode, press <Esc>. The data value shown is the actual data value stored at that location in the workspace.

For ND spectra, accurate peak positions and heights can be read interactively from the display using this menu item. When you select the Measure/Cursor Position command, FELIX displays a crosshair cursor and reports the cursor position in x- and y-axis units (possibly the third and fourth dimension, as well); FELIX also reports the matrix value at that point.

FELIX continuously updates the information as you move the cursor, until you quit the cursor-tracking mode by pressing <Esc>.


Measure/Correlated Cursors

Use the Measure/Correlated Cursors (<Alt>+uc) command to initiate a multiple-cursor mode. Use this mode to correlate peaks in more than one simultaneously displayed plot. For example, you may plot a TOCSY, COSY, and NOESY spectrum in three different frames. When you select the Measure/Correlated Cursors command and move the cursor into one of the frames, the cursor becomes a crosshair cursor and crosshair cursors appear and track the identical positions in the other two frames. If the matrices are referenced and displayed with axis units of ppm, use the cursors to correlate peaks in the three spectra. Press the mouse button to report the current position. To quit multiple-cursor mode, press <Esc>.


Measure/Distance/Separation

For a 1D spectrum, in addition to spectrum positions and intensities, you can calculate the separation between any two spectrum features in a display using the Measure/Distance/Separation command (<Alt>+ud). Use a crosshair cursor to select two locations on the display. FELIX reports the separation in points, ppm, and Hertz. To exit, press <Esc>.

For an ND spectrum, use the Measure/Distance command to find the distance between the two atoms defining a particular peak (either through peak assignment or through frequency assignment) by clicking the peak. FELIX measures the distance in the currently active molecule.


Measure/Integral/Volume

1D Integral

You may use FELIX to integrate the entire spectrum as a single integral or as shorter segments. To integrate the entire spectrum, select the View/Draw Integrals command (<Alt>+vs). If you want additional options dealing with integrals, use the Measure/Integral/Volume command (see below).

Use the Add button to define integral segments. Add integral segments by dragging out a segment region with the mouse. To exit this mode, press the <Esc> key. FELIX displays integral curves after exiting the add segment mode.

If you make a mistake while selecting individual segments or if you want to modify the current list of segments, you may delete a small subregion of segments graphically. Click the Remove button to create a small crosshair cursor. Then drag out a region of segments to delete.

To delete all the segments, click the Remove All button in the Measure/Integral/Volume command. This deletes the current integral segments entity from the database and requires confirmation via a dialog box.

Click the Draw button to redraw the integrals curves. Click the Dismiss button to remove the integral curves from the plot.

Click Adjust to adjust the display of the integrals. FELIX displays another dialog. Here you can select different display types, adjust the slope, bias, or overlap of the integral curves.

Note: By adjusting the slope and bias, you can set an integral value to any value. Use these adjustments cautiously.

Click the Normalize button if you want to normalize the display values of the integrals.

ND volume measurement

FELIX calculates the volume of a cross peak as the integral of all data-point intensities inside the cross-peak footprint. The reserved symbol hafwid controls the relative size of all footprints, affecting the resultant volume measurements. (Please see the FELIX Command Language Reference Guide for more detailed information about this symbol).

Because the peak picker determines the cross-peak footprint widths from the peak's half-width at half-height, tall peaks, which have better signal-to-noise ratios, have relatively smaller footprints than small peaks with worse signal-to-noise (and thus relatively larger footprints). In this way, the volume of a strong peak is the sum of relatively few data points of high intensity, while the volume of a weak peak is the sum of relatively many data points of low intensity.

Use the Show One Volume option to calculate and display the volume of a single cross peak. The arrow cursor becomes a large crosshair; use it to click the peak of interest. FELIX calculates the volume for the selected cross peak and displays it in the output window. When there is a current volume entity, FELIX displays both the raw calculated volume and the stored volume from the volume entity. As long as a peak is selected, FELIX repeats the action. To end the action, click in a region of no peaks or press <Esc>.

Use the Measure All Volumes option to measure the volumes of all cross peaks. FELIX displays a control panel and prompts you to specify the cross peak entity name, the volume entity name, a slot number, and the mixing time for the current matrix in seconds. If the named volume entity does not yet exist, FELIX prompts you to specify the total number of slots to be built into the new volume entity. When the volume entity does exist, FELIX first checks to make sure that the number and IDs of all cross peaks match the number and IDs of all volumes. This assures that the two entities are compatible. Specifying a slot number that you have already used overwrites those volumes.

The measured volumes depend on the center and width of each cross peak and the reserved symbol hafwid, which can be adjusted using the Preference/Peak Display command. Measuring volumes is very fast for small cross-peak sets, but can take tens of seconds for very large numbers of cross peaks.

Use the Measure Buildups option to measure the volumes not only in one spectrum but in a series of spectra within the same buildup. It stores the result in the consecutive slots of the same volume entity.

Use the Remeasure Buildup for One Peak option to remeasure a buildup for a particular peak.

Use the Delete Volumes option to delete the current volume entity, after prompting you for confirmation. There is no way to delete a portion of the volumes.


Measure/Buildup

Measure/Buildup/Show Buildup

Use the Measure/Buildup/Show Buildup (<Alt>+ubs) command to display a graphical representation of all the stored volume slots for a selected cross peak. Select a cross peak with the large crosshair cursor. FELIX produces a 2D graph of volume versus time, showing the volume buildup for that cross peak. The initial datapoint of zero volume at time zero is explicitly included.

Measure/Buildup/Fit Buildup

Use the Measure/Buildup/Fit Buildup (<Alt>+ubf) command to fit the buildup data to any of seven different functions.


Measure/J Coupling

FELIX provides a set of tools for extracting J-coupling constants from a variety of spectra. These coupling constants then can be used to calculate torsion angle restraints for structure determination studies.

Because of the complexities of overlapping COSY peaks and multiplet "splitting" effects within any one peak, you can calculate the J-coupling constants for only one peak at a time. Based on the quality of the results, you are then free to add each J-coupling measurement to the J-coupling entity one at a time.

Measure/J Coupling /DQF

The Measure/J Coupling/DQF (<Alt>+ujd) command uses a sophisticated line-fitting algorithm to calculate the true centers of each lobe of a DQF-COSY multiplet and then measures the separation in Hertz. This command works only on non-overlapping peaks with four primary lobes (down, up, up, down). It cannot robustly handle peaks with more lobes due to "splitting". Use a crosshair cursor to select a peak. FELIX then calculates and reports the J coupling and sigma in the output window.

The algorithm works as follows:

1.   For each dimension, FELIX divides the cross-peak footprint in half and then projects each half (sum the points) down to a 1D line segment. This yields two 1D line segments; each represents the line shape of two lobes of the cross peak (one up, one down). The number of datapoints in each line segment depends on the size of the cross-peak footprint in that dimension.

2.   Next, each of these line segments is peak-picked (to yield two peaks;  one positive, one negative) and then passed through the 1D curve fitter to optimize the two peak centers, widths, and heights to best-fit Gaussian line shape models. This optimization step is responsible for finding the "true" centers from the "apparent" centers given by the peak-pick routine, for each line segment. This yields two independent measurements for the separation in each dimension.

3.   FELIX reports the average separation as the J-coupling value and reports the deviation from that average as the sigma, or uncertainty, of that J-coupling value, for each dimension.

Manual ECOSY

Use the Measure/J Coupling/Manual ECOSY command (<Alt>+ujy) to measure a coupling between two subpeaks of a typically ECOSY spectrum. Use the cursor to define the boundaries of two subpeaks; then, FELIX uses the optimizer (similar to DQF) to measure the distances.

Heteronuclear ECOSY

Use the Measure/J Coupling/Heteronuuclear ECOSY command (<Alt>+uje) to measure J couplings in heteronuclear ECOSY-type 2D experiments (Griesenger et al. 1986).

Heteronuclear FIDS

Use Measure/J Coupling/Manual FIDS command (<Alt>+ujf) to measure a 3J coupling on two HSQC spectra using the FIDs (fitting of doublets and singlets), where you measure the fully decoupled and a partially coupled HSQC spectrum. After peak picking, the coupling constants can be extracted using time-domain fitting (Schwalbe et al. 1993).

Heteronuclear FIDS/ECOSY

Use the Measure/J Coupling/Heteronuuclear FIDS/ECOSY command (<Alt>+ujs) to measure the 2JCN and 3JCN coupling constants on three 2D HSQC experiments, using the combined C1-FIDS or FIDS-ECOSY method (Rexroth et al. 1995a).

Heteronuclear DQ/ZQ

Use the Measure/J Coupling/Heteronuuclear DQ/ZQ command (<Alt>+ujz) to measure the J couplings on a pair of double-quantum and zero-quantum 2D experiments like HN(CO)CA or HNCA (Rexroth et al. 1995b).

Heteronuclear 3D ECOSY

Use the Measure/J Coupling/Heteronuuclear 3D ECOSY command (<Alt>+uj3) to measure the J couplings in a 3D ECOSY-type experiment.

HSQC-J

Use the Measure/J Coupling/HSQC-J command (<Alt>+kjh) to measure the J coupling via a series of HSQC experiments, finding the coupling constant by interpolating the zero crossing of the volume series.

Note: You must have picked peaks in a series of HSQC spectra and have measured volumes measured and stored them in the volume entity.

Manual Separation

The Measure/J Coupling /Manual Separation (<Alt>+ujm) command is a primitive tool, compared to the line-fitting algorithm described above. You select a peak with a large crosshair cursor. FELIX plots the chosen peak in an expanded blown-up frame to represent as much peak shape as possible. Then, use a small crosshair to drag out a rectangular shape. Try to align the four corners of the rectangle on the true centers of the four lobes of the peak. Measure/J Coupling /Manual Separation then calculates the separation in Hertz from your cursor corners and reports the J-coupling values in the output window. There are no sigma terms with this method, since there is only one measurement for each dimension.

Volume Ratio

Use the Measure/J Coupling/Volume Ratio command (<Alt>+ujv) to display the volumes of two peaks (e.g., an off-diagonal and a diagonal) selected via the cursor from the currently displayed ND spectrum (usually triple resonance). Use this volume ratio for calculating J coupling with an external program.


Measure/Relaxation

The Measure/Relaxation menu offers a suite of tools that allow you to analyze a series of heteronuclear 2D relaxation spectra. FELIX assumes that peaks have been picked in one of the spectra or in a similar one with the same spectral widths.

Measure Heights/Volumes

Use the Measure/Relaxation/Measure Heights/Volumes command (<Alt>+uv) to evaluate peak heights or volumes in the series of spectra. This feature includes optimization options to accommodate slight peak displacements relative to the initial peak table and moderate peak overlaps.

S/N Ratio

Use the Measure/Relaxation/S/N Ratio command (<Alt>+us) to determine the signal-to-noise ratio by analyzing one or more duplicate spectra and extrapolating to the remaining time points.

View Timecourse via Cursor

Use the Measure/Relaxation/View Timecourse via Cursor command (<Alt>+uc) to point at a peak in the displayed 2D spectrum and display the series of peak heights or volumes of that peak with error bars as determined by the previous two menu options. FELIX also displays the best-fit exponential decay curve if one has been fitted to the data, and displays the relaxation rate in the status bar and the output window.

View Timecourse via Item

Use the Measure/Relaxation/View Timecourse via Item command (<Alt>+ut) to choose a peak number whose time course you want displayed.

Fit R1/R2/NOE

Use the Measure/Relaxation/Fit R1/R2/NOW command (<Alt>+uf) to analyze the peak height or peak volume data. FELIX fits the R1 and R2 timecourses to appropriate exponential decay curves, taking into account the experimental uncertainties. FELIX displays the resulting relaxation rates in the output window and stores them in a database table. The database table also holds the other parameters of the fitted curve in order to reconstruct it if necessary. FELIX evaluates the heteronuclear NOE by taking the ratio of the peak heights in spectra acquired with 1H saturation and without 1H saturation. Signal-to-noise evaluation is built into this procedure by analyzing a second pair of spectra.

Modelfree input

Use the Measure/Relaxation/Modelfree Input command (<Alt>+um) to extract the relevant parameters from the FELIX database and prepare a rudimentary input file for the ModelFree program of A.Palmer (available at
http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/).


Measure/Scalar/Normalize

FELIX can normalize the integral of any segment of the spectrum to an arbitrary value. Four normalization menu items are available under the Measure/Scalar/Normalize command (<Alt>+un). After normalization, FELIX updates the volume element in the integral segment entity to the normalized value.

Note: This function can also be accessed directly from the Measure/Integral/Volume command for 1D spectrum.

By Item Number of Segment

Use the By Item Number of Segment command to create a list box where you graphically select the segment to normalize based on its beginning and ending point. You must also give a normalization value for this segment.

By Data Point Limits

Use the By Data Point Limits command to display a control panel in which you enter a low and high point to define a normalization range, as well as the normalization value.

Select Segment via Cursor

Use the Select Segment via Cursor command to generate a small crosshair cursor to select the segment to normalize by dragging to enclose the segment.

Raw Absolute Integrals

Use the Raw Absolute ntegrals command to store and display each segment's integral as its raw intensity, with no normalization at all.

The rate of volume buildup for a cross peak in a set of NOESY matrices is related to the distance between the two corresponding atoms in the molecule of study. Before deriving distance restraints from a set of volume buildup rates, you must define a scaling constant taken from cross peaks that correspond to fixed interatomic distances in the molecule. Define a small set of reference cross peaks that all correspond to a single fixed distance. FELIX then averages the buildup rates of these peaks to determine the scaling constant used to convert volume buildup rates into distance restraints.

Note: Due to the method of averaging these rates, it is very important that all cross peaks selected as scalar peaks correspond to one single interatomic distance in angstroms. The only exception to this rule is when the Empirical Fit method of restraint calculation is used. Here, the scalar entity consists of a series of scalar peaks that correspond to a range of interatomic distances.

Note: We cannot overemphasize the importance of these reference peaks: they are crucial in defining NOE distance restraints.

Add One

Use the Measure/Scalar/Normalize/Add One command to add one more cross peak to the scalar peak entity. FELIX displays a control panel and prompts you for the assignment names in D1 and D2 and a distance in angstroms. FELIX then searches the current cross-peak entity for a peak with those names, verifies that peak is not already a scalar, and then adds one more entry to the scalar-peaks entity.

Note: Remember that all scalar peaks should represent one single distance. Basing the scaling constant on an average of different distances is not valid. The only exception to this rule is when the Empirical Fit method of restraint calculation is used (see above).

Add One via Cursor

Use the Measure/Scalar/Normalize/Add One via Cursor command to add the peak by selecting it with the cursor.

Delete One

Use the Measure/Scalar/Delete One command to remove one peak from the scalar entity. FELIX displays a control panel and shows you a list of all scalar peaks, by assignment name. Select one scalar to remove from the entity. Repeat this action to delete other scalar peaks.

Clear All

Use the Measure/Scalar/Clear All command to delete the entire scalar-peaks entity. FELIX prompts you for confirmation.

Change

Use the Measure/Scalar/Normalize/Change command to displays a control panel that shows the name of the current scalar entity. Only one scalar entity can be current at a time. To change to another scalar entity, enter a different name and click OK.

Normalize/View

Use the Measure/Scalar/Normalize/View command to create a spreadsheet of the scalar entity. Here you view the individual scalar peaks and interatomic distances. In the spreadsheet, you can edit the distance.


Measure/DISCOVER Restraints

One of the principal goals of analysis of 2D NOESY experiments is accumulating interatomic distance restraints for use in various molecule structure-determination studies. FELIX provides a set of menu items for turning volume buildup rates into distance restraints. Once you have an entity of scalar peaks, you are ready to generate distance bounds from assigned cross peaks. You can generate restraints in DGII/Discover format or in XPlor format, using the Measure/DISCOVER Restraints and Measure/X-PLOR Restraints commands, respectively.

Several restraint classes are supported in FELIX. The basic 2D NOESY peaks can be used in structure generation and refinement as NOE-distance restraints. Based on an assigned peak entity and measured volumes (optionally buildups), FELIX can create new restraints, interactively show one restraint, and use a list of violations to recalculate restraints.

NOE Distance Define

Use the NOE Distance Define option to create a new entity (msi:noe_dist) of distance restraints from volume buildup rates. Defining restraints overwrites any existing restraints if Action in the control panel is set to New. If Action is set to Append, the restraints produced are appended to the restraint entity. The entity name containing the scalar information used in calculating the restraints is then input. You then input values for the Lower Force Constant, Upper Force Constant, and Maximum Force. Then you select the method used to derive the buildup rates. You can choose between using a Single mixing time or a "best fit" rate based on the First N mixing times, as calculated by a first-order polynomial (Straight Line), a Second Order Polynomial, or an Empirical Fit. In an Empirical Fit calculation, FELIX uses a scalar entity containing a series of cross-peak intensities that correspond to a range of interatomic distances to determine an empirical relationship between NOE intensity and distance.

Although NOE volumes, in reality, increase exponentially and are damped by the exponential T2 relaxation, there are simply not enough mixing times to yield a robust fit to such an exponential-type function. Since only the initial buildup rate is needed (not the entire function), FELIX provides fit functions that can robustly calculate the initial rate from a small set of volume observations.

You can define, for the case of a symmetric spectrum, which peaks are to be considered in the restraint generation: all peaks or peaks on a specific side of the diagonal (for up to three user-defined regions) or only the lower-intensity peaks (symmetry selection).

All the above methods (except Empirical Fit) use the inverse 6th-power relation between buildup rate and interatomic distance to calculate a single distance in angstroms from the volume buildup rate for each cross peak and the scaling constant derived from the scalar peaks. That one resultant distance is then used to create a restraint having lower and upper distance bounds, based on the chosen method.

Use the Exact Distance method to create an entity where each restraint is an exact distance. FELIX displays a control panel that prompts you to specify the minimum and maximum distance allowed for any restraint. For all restraints, the lower- and upper-bound distances are both set to the one calculated distance.

Use the Strong-Medium-Weak Bins method to create an entity where each restraint is grouped into one of three distance-bound bins. FELIX displays a control panel that prompts you to specify the minimum and maximum distances allowed, the distance boundary between the strong and medium bins, and the distance boundary between the medium and weak bins. For all restraints, the lower and upper bounds are one of these three explicit distance ranges, depending on which bin the calculated distance falls in.

Use the Van Der Waals-Exact method to create an entity where each restraint uses a generic van der Waals hard-sphere radius for the lower bound and sets the upper bound to be the calculated distance. FELIX displays a control panel that prompts you to specify the van der Waals lower bound and the maximum upper bound.

Use the Percentage of Distance method to create an entity where each restraint uses a percentage of the calculated distance as the lower and upper bounds. FELIX displays a control panel that prompts you to specify the minimum and maximum distances, a lower-bound percentage, and an upper-bound percentage. For each restraint, the lower bound is determined by subtracting the lower-bound percentage of the calculated distance from the calculated distance, while the upper bound is obtained by adding the upper-bound percentage of the calculated distance to the calculated distance. In this manner, short distances translate into narrower bounds while longer distances have wider bounds.

Also, you may specify that only the non-overlapped peaks be used in creating restraints. You can choose what percentage of the peak box area overlap is to be handled differently, by setting the Area Threshold. You can then discard those peaks (set Partial Overlap to Discard) or use a different method to turn them into restraints (e.g., Use as Qual).

NOE Distance Calculate One

The NOE Distance Calculate One command is similar to the NOE Distance Define command above, except that only a single restraint is calculated and the restraint value is not saved to the database. Use the cursor to specify the cross peak used in the restraints calculation.

NOE Distance Redefine

The Measure/DISCOVER Restraints/NOE Distance Redefine command serves as a refinement tool. After a set of peaks is assigned and a set of restraints is extracted based on that assignment, you can try to generate structures by using distance geometry (Insight II/NMR_Refine/DGII) or simulated annealing (Insight II/NMR_Refine/MD_Schedule).

After a successful run, several hot-spots are normally discovered; for example, certain assignments or restraints may not be right. If so, use the NOE Distance Redefine command to loosen, tighten, or delete some restraints showing the highest violations (or the highest number of violations within a family). To do this, you must first load the restraints on all the refined molecules into to the Insight II program, using the NMR_Refine/Restraints/Read molname* command.

Then you may execute the NMR_Refine/Distance/List command. The provided numvioltofelix script redirects the output into another file.

At this point, you can use the Measure/DISCOVER Restraints/NOE Distance Redefine command on this file. You should specify the Restraint entity you want to work with (usually the accelrys:noe_dist) and the Buildup Rate Calculation Method.

FELIX next shows the violation table, from which you can zoom in on each peak for which the defined restraint was violated. From the table you can see the calculated distance, the restrained values, and the violation statistics. You then can select an Action: Leave as is, Redefine bounds, Delete Restraints.

NOE volume Define

From an assigned peak entity and the corresponding volume entity, FELIX can calculate NOE volume restraints, which contain volume lower bounds and upper bounds as restraining entities. These can then be used in Discover.

Use the NOE Volume Define command to calculate and stores NOE-volume restraints for all the assigned peaks.

NOE Distance Overlap Define

In certain instances some peaks can have multiple possible assignments. Those assignments (made in Assign) can be used in Discover to help in the refinement. These restraints are called NOE distance overlapped restraints.

You must have already defined singly assigned peaks as scalar peaks and also have defined the volumes to be measured before you can generate overlapped restraints. You can use the NOE Distance Overlap Define option to define such restraints from 2D NOE spectra or from heteronuclear edited 3D or 4D NOE spectra. Each NOE distance overlap restraint contains a set of possible atom name pairs (multiple possible assignments), as well as an effective distance upper and lower bound. You can export these restraints to the Insight II program and use them as ambiguous restraints in a Discover simulated annealing or rMD, rEM run.

NOE Volume Overlap Define

The peaks with multiple possible assignments can be used in Discover directly - that is, without turning them into effective distances - to help in the refinement. These restraints are called NOE volume overlapped restraints.

You must have already measured the volumes (buildups) before you can generate overlapped restraints. You can use the NOE Volume Overlap Define option to define such restraints from 2D NOE spectra or from heteronuclear edited 3D or 4D NOE spectra. Each NOE volume overlap restraint contains a set of possible atom name pairs (multiple possible assignments), as well as restraining volume(s). You can export these restraints to the Insight II program and use them as ambiguous restraints in a Discover simulated annealing or rMD, rEM run.

3J Dihedral

After measuring 3J couplings using the above described menu items and then assigning peaks, use the 3J Dihedral option to create 3J-dihedral restraints.


Measure/X-PLOR Restraints

NOE

Several restraint classes are supported in FELIX. The basic 2D NOESY peaks can be used in structure generation and refinement as NOE-distance restraints. Based on an assigned peak entity and measured volumes (optionally buildups), FELIX can create new restraints, interactively show one restraint, and use a list of violations to recalculate restraints.

Use the Define option to create a new entity (msi:noe_dist) of distance restraints from volume buildup rates.

Defining restraints overwrites any existing restraints if the Action parameter is set to New.

If Action in the control panel is set to Append, FELIX appends the restraints produced to the restraint entity. Next, input the entity name containing the scalar information used in calculating the restraint. Then you select the method used to derive the buildup rates. You can choose between using a Single mixing time or a "best fit" rate based on the First N mixing times, as calculated by a first-order polynomial (Straight Line), a Second Order Polynomial, or an Empirical Fit. In an Empirical Fit calculation, FELIX uses a scalar entity containing a series of cross peak intensities that correspond to a range of inter-atomic distances to determine an empirical relationship between NOE intensity and distance.

Although the NOE volumes, in reality, increase exponentially and are damped by the exponential T2 relaxation, there are simply not enough mixing times to yield a robust fit to such an exponential-type function. Since only the initial buildup rate is needed (not the entire function), FELIX provides fit functions that can robustly calculate the initial rate from a small set of volume observations.

You can define, for the case of a symmetric spectrum, which peaks are to be considered in the restraint generation: all peaks or peaks on a specific side of the diagonal (for up to three user-defined regions) or only the lower-intensity peaks (symmetry selection).

All the above methods (except Empirical Fit) use the inverse 6th-power relation between buildup rate and interatomic distance to calculate a single distance in angstroms from the volume buildup rate for each cross peak and the scaling constant derived from the scalar peaks. That one resultant distance is then used to create a restraint having lower and upper distance bounds, based on the chosen method.

The Exact Distance method creates an entity where each restraint is an exact distance. A control panel asks for the minimum and maximum distances allowed for any restraint. For all restraints, the lower- and upper-bound distances are set to one calculated distance value.

The Strong-Medium-Weak Bins method creates an entity where each restraint is grouped into one of three distance bound bins. A control panel prompts you for the minimum and maximum distances allowed, the distance boundary between the strong and medium bins, and the distance boundary between the medium and weak bins. For all restraints, the lower and upper bounds are one of these three explicit distance ranges, depending on which bin the calculated distance falls in.

The Van Der Waals-Exact method creates an entity where each restraint uses a generic van der Waals hard-sphere radius for the lower bound and sets the upper bound to be the calculated distance. A control asks prompts for the van der Waals lower bound and the maximum upper bound.

The Percentage of Distance method creates an entity where each restraint uses a percentage of the calculated distance as the lower and upper bounds. A control panel prompts you for the minimum and maximum distances, a lower-bound percentage, and an upper-bound percentage. For each restraint, the lower bound is obtained by subtracting the lower-bound percentage of the calculated distance from the calculated distance, and the upper bound is obtained by adding the upper-bound percentage of the calculated distance to the calculated distance. In this manner, short distances are translated into narrower bounds, and longer distances have wider bounds.

You may specify that only non-overlapped peaks be used in creating restraints. You can choose what percentage of the peak box area overlap is to be handled differently by setting the Area Threshold parameter. You can then discard those peaks (set Partial Overlap to Discard) or use a different method to turn them into restraints (for example, Use as Qual).

Ambiguous NOE

In certain instances some peaks can have multiple possible assignments. Those assignments (made in Assign) can be used in XPlor to help in the refinement. These restraints are called ambiguous NOE restraints.

You must have already defined singly assigned peaks as scalar peaks and also have defined the volumes to be measured before you can generate overlapped restraints. You can use the Ambiguous NOE and Define options to define such restraints from 2D NOE spectra or from heteronuclear edited 3D or 4D NOE spectra. Each ambiguous NOE restraint contains a set of possible atom name pairs (multiple possible assignments), as well as effective distance upper and lower bounds. You can export these restraints to the Insight II program and use them as ambiguous restraints in a XPlor simulated annealing or rMD, rEM run.

Dihedral

After measuring 3J couplings using the above described menu items and assigning peaks, you can create dihedral restraints using the Dihedral option.

NOE-Intensity

Using an assigned peak entity and the corresponding volume entity, FELIX can calculate NOE intensity restraints, which contain volume lower and upper bounds as restraining entities in the NOE-Intensity and Define options. These can then be used in XPlor.

Ambiguous NOE-Intensity

Peaks with multiple possible assignments can be used in XPlor directly (that is, without turning them into effective distances) to help in the refinement. These restraints are called ambiguous NOE-intensity restraints.

You must have already measured the volumes (buildups) before you can generate overlapped restraints. You can use the Ambiguous NOE-Intensity and Define options to define such restraints from 2D NOE spectra or from heteronuclear edited 3D or 4D NOE spectra. Each ambiguous NOE intensity restraint contains a set of possible atom name pairs (multiple possible assignments), as well as restraining volume(s) bound. You can export these restraints to the Insight II program and use them as ambiguous restraints in an XPlor simulated annealing or rMD, rEM run.

NOE-NOE

If you have an assigned 3D NOE-NOE spectrum where you measured volumes, you can turn them into 3D NOE-NOE restraints using the NOE-NOE and Define options.


Window pulldown

The Window pulldown (<Alt>+W) contains commands that rearrange or reset the frames for spectral display.


Window/Cascade

The Window/Cascade command (<Alt>+wc) allows you to rearrange the windows by cascading them.


Window/Tile Horizontally

The Window/Tile Horizontally command (<Alt>+wh) allows you to rearrange the windows as horizontal tiles.


Window/Tile Vertically

The Window/Tile Vertically command (<Alt>+wv) allows you to rearrange the windows as vertical tiles.


Window/Add New Window

The Window/Add New Window command (<Alt>+ww) allows you to add a new spectral frame.

Note: If there is an existing spectral frame, the newly opened frame inherits all the reserved and user-defined symbols from it.


Window/New Layout

The Window/New Layout command (<Alt>+wn) allows you to remove all the current frames, and create a new set of frames.

Note: The New Layout options delete the contents of existing spectral frames.


Help pulldown

The Help pulldown (<Alt>+h) contains commands that provide information on using FELIX.


Help/About

The Help/About command (<Alt>+ha) gives you information about the current version of FELIX.


Help/Topic

The Help/Topic command (<Alt>+ht) opens a Netscape browser window and allows you to access the online documentation.


Help/Keypad

The Help/Keypad command (<Alt>+hk) gives you information about the currently available navigation commands and their keypad shortcuts.