The processing, visualization, and analysis functions in FELIX are accessible throughout the interface. The menu items specific to any mode other than this basic one (for example, those in the Model and Assign modules) are described in later chapters.
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. A description of each general menu item in the File pulldown follows.
The File/New menu item (<Alt>-fn) creates a new database file or a new matrix. Selecting the menu item 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. You should enter the name of the file in the Selection box. If you want to build a matrix, you must set up the sizes and select the appropriate dimension.
The File/Open menu item (<Alt>-fo) can open an existing datafile for processing and analysis or can open an existing database file, matrix, molecule, or macro for execution. Before you can perform any operations on a data matrix, you must open the data using this menu item. Selecting the menu item 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 old- or new-FELIX format, Bruker files from AMX or newer spectrometers (ser or fid), Varian fid files, JEOL Alpha or Delta files, or FELIX for Windows FID files. If you want to read in FELIX old-format data, you must 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, the current database is closed and the newly selected one opened. If the old database has changed in some way, then after you select the new database, the program asks you whether to save the changes.
The File/Save menu item (<Alt>-fs) allows you to save the current database or the current data in the workspace to disk. In some instances, you might want to save the data by writing it to disk and creating a permanent record. If the file already exists, you are asked whether to quit or overwrite the file.
The File/Save As menu item (<Alt>-fa) allows you 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, you are asked whether to quit or overwrite the file. The new database now becomes the current database.
The File/Close menu item (<Alt>-fc) allows you to close the current database, the current data in the workspace, or the current matrix. For a write-enabled matrix, the current parameters (displayed limits, display type, current entities) are stored in the header. These parameters are used the next time you open this matrix to set the limits, display color, peak, and other entities.
The File/Import (<Alt>-fi) menu item generates a pullright menu of controls used to import database entities of tables, including a generic table-import menu item and some special table-import menu items.
The File/Import/Table (<Alt>-fit) menu item attempts to read an ASCII file from disk into the binary FELIX database. This action is very format specific, so be certain that the entity file you read is in an acceptable format. You have to select an ASCII table file in the Selection and set the Table Name to an entity that will be created in the database file.
The File/Import/Peaks menu item (<Alt>-fip) allows you to read an ASCII file that contains peak information into the peak entity. You are asked for an input filename as well as an entity name. Supported formats include FELIX peak entity format, Insight II .pks and .asn formats, NMRCompass peak file (.dat), and a new ASCII format.
The File/Import/Plot Limits menu item (<Alt>-fil) allows you 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 menu item.
The File/Import/Restraints (<Alt>-fir) menu item imports database information from the format supported by Insight II into the FELIX database. For more information, please see the Tasks chapter.
The File/Import/Scalars menu item (<Alt>-fis) allows you to read an entity containing scalar peaks from disk.
The File/Import/Spin Systems menu item (<Alt>-fiy) allows you to read in spin systems if an Assign project is open. The supported formats include: FELIX pattern ASCII file, Insight II resonance (.ppm) file, and NMRCompass assignment table (.dat). Performing this action destroys any current spin-system (pattern) information in the database.
The File/Import/Theoretical (<Alt>-fih) menu item imports database information - back-calculated using IRMA or Matrix Doubling in Insight II/NMR_Refine - from the format supported by Insight II into the FELIX database.
The File/Import/Buildup (<Alt>-fib) menu item imports a volume or intensity buildup curve into the workspace.
The File/Export (<Alt>-fe) menu item generates a pullright menu of controls used to export database entities of tables, including a generic table-export menu item and some special table-export menu items.
The File/Export/Table (<Alt>-fet) menu item writes a FELIX database entity to an ASCII file on disk. In the first control panel, you select an existing entity. In the next control panel, you enter an ASCII table file as the Selection.
The File/Export/Peaks menu item (<Alt>-fep) allows you to write the peak entity into an ASCII file that contains peak information. You are asked for a filename as well as the current peak entity name. The supported formats include: FELIX peak entity format, Insight II .pks and .asn formats, a new ASCII file of all peaks or only of the assigned peaks. These latter two files can contain peaks with multiple competing assignments if the peak assignments were done through the Assign module.
The File/Export/Plot Limits menu item (<Alt>-fel) allows you to write out the current plot limits of the displayed matrix.
The File/Export/Restraints (<Alt>-fer) menu item exports FELIX database information to the format supported by Insight II. The restraints exported can be either in Discover/DGII format or in X-PLOR format. For more information on this feature, please see the Tasks chapter.
The File/Export/Scalars menu item (<Alt>-fes>) allows you to write the current scalar entity to disk.
The File/Export/Spin Systems menu item (<Alt>-fey) allows you to write the spin systems (patterns) to disk if an Assign project is open.
The File/Export/Buildup (<Alt>-feb) menu item exports a volume or intensity buildup curve from the workspace to the disk.
The File/Convert (<Alt>-ft) generates a pullright menu of converting (filtering) controls. You can convert an unprocessed spectrometer datafile or a processed matrix.
The File/Convert/Data (<Alt>-ftd) menu item converts unprocessed spectrometer data from formats that FELIX can filter (translate) into the FELIX data format. This makes a new FELIX-format datafile, which can later be read into the program. Some of these filters allow explicit byte swapping to be forced or overridden, to provide the greatest level of flexibility when trying to read the native datafile. The data-filter function requires the spectrometer datafiles to be in their native form (for example, a directory of raw data and parameter files constitutes one data file on Varian spectrometers). These formats are supported:
The Bruker X32/Aspect1, Varian, and JEOL Alpha and Delta data can be opened and read directly into FELIX without conversion - please see the File/Open menu item description.
The File/Convert/Matrix (<Alt>-ftm) menu item converts 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:
You can create a BioMagResBank deposition file from an existing Assign project using the File/BMRB menu item (<Alt>-fb). The project should be open, and the assigned resonances are output as a deposition form that can be sent to BioMagResBank.
The File/Print menu item (<Alt>-fp) generates a hardcopy plot of the spectra in the current frame. FELIX can generate high-quality hardcopy output on different devices, including laser printers (including all PostScript devices) and pen plotters (including plotters that support the HPGL format). To generate a hardcopy plot, select the Hardcopy menu item and fill in the resulting control panel.
Since each of the output devices reads a very specific plotfile format, you must first tell FELIX which type of output is required for your printer or plotter. This is done by selecting either PostScript or HPGL as the Plot device.
Once the hardcopy plot device has been defined, you must tell FELIX where to send the output. The destination in the Output File box directs the hardcopy plot output to a specified computer port (serial or parallel) or to a filename. The computer ports most commonly used to connect your computer to the printer/plotter are indicated below. If you have customized your computer system, these port names may be different. You may need to consult with your system manager before filling in this box.
If you want to direct the hardcopy plot output to a file, fill in the Output File box with the desired filename. After the hardcopy plot file is created, you need to use operating-system commands to send the plot file to the desired device. For example, on a Sun workstation, you would enter:
> % cat temp.plt > /dev/ttya
to get a hardcopy of your data on a plotter connected to the /dev/ttya port. The cat command is an operating-system command, not a FELIX function. Therefore, you must either exit FELIX to execute the cat command or open a separate shell window and execute the command from there. Similarly, the sys command can be used to communicate with your operating system.
You should use an output file or specify a print command rather than directly specifying a hardware port or device name. The risk of data overrun, poor hardware handshaking, and clashing with other jobs in the printer queue are very high. You get better results by specifying a print command and letting the operating system control the flow of data to the printer or plotter.
In addition to defining the output file format and where the output is to be directed, there are several other options you may set. You may set the origins or the plot size in inches or centimeters by selecting the appropriate toggle. You also can specify the aspect ratio of the final plot. If you set the Aspect ratio to Free, then the aspect ratio of the plot corresponds to that of the original data., although the data are scaled to fit within the x and y sizes specified. If you set the Aspect ratio parameter to Fix, then the aspect ratio of the plot is determined by the x and y size parameters that you specify. For PostScript or HPGL plots, you may define whether the plot has a Landscape or Portrait orientation. For PostScript plots, you may define whether the plot uses an RGB (color) or Grayscale colormap, and Stroke or PostScript Font characters. For HPGL plots it is important to specify whether your plotter defines the Origin at the Center or the Corner of the plot.
It is often desirable to switch between different predefined plot layouts. The Parameter File menu item allows you to easily save a particular plot layout and to quickly switch between several plot styles. If the Parameter File menu item is set to No, then the Hardcopy menu item behaves normally and a plotfile is produced. If the Parameter File option is set to Read, then a parameter file is read in and the various controls in the panel are set as specified in the file. If the Parameter File option is set to Write, then a parameter file is written out with the current state of the various Hardcopy control-panel options. A plot file is produced only when the Parameter File option is set to No.
After defining all the hardcopy parameters, simply select OK to generate a plot or plotfile.
The File/Licenses menu item (<Alt>-fl) allows you to release any features that you don't currently need, allowing others in your workgroup to use them. Also, if one feature was not available when you started FELIX but became available later, you can check it out later using this function.
The File/Exit menu item (<Alt>-fx) exits FELIX. If changes have been made to the FELIX database, a dialog box asks you whether to Save the database and exit and whether to Save the current environment (which can be restored later).
The most common way to manipulate displays is to access the View pulldown.
To redraw the current workspace, select the View/Plot menu item (<Alt>-vp or <Ctrl>-p).
FELIX displays NMR data as 1D slices, a 2D intensity plot, a 2D contour plot, a 2D stack plot or 3D pseudo-cube display of a 3D matrix, or a 3D sub-cube of a 4D matrix. In the intensity plot, data values above a set contour level are presented as a filled rectangular region. The intensity plot is drawn more quickly and coarsely than a contour plot, so 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. 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. Stack plots display the matrix as a series of 1D plots that are drawn in sequence with x and y offsets and removal of hidden lines. The resulting plot resembles the projection of a 3D relief map onto a 2D surface and provides a qualitative display that may be useful for evaluating the baseline.
To select a type of plot other than the current one, select the View/Plottype menu item (<Alt>-vt). This displays a menu of all the valid plot types. To display the current workspace (1D spectrum, 1D slice of an ND spectrum, x-y pairs, etc.) select the View/Plottype/1D (<Alt>-vt1 or <Ctrl>-1) menu item. To display an intensity plot, select the View/Plottype/Intensity (<Alt>-vti or <Ctrl>-i) menu item. For a contour plot, select the View/Plottype/Contour (<Alt>-vtc or <Ctrl>-c) menu item. Likewise the View/Plottype/Stack (<Alt>-vts) menu item displays a stack plot, while the View/Plottype/Null (<Alt>-vtn) menu item displays a null plot. You can overlay contour plots if multiple spectra were defined as experiments in Assign and you set which experiments should contribute to the overlay plot (Preference/Overlay) using the View/Plottype/Overlay (<Alt>-vto) menu item. After selecting a new type of plot with the Plottype menu item, the plottype popup in the iconbar automatically renames itself to show the new default type of plot.
Since FELIX always performs its processing and analysis actions on the currently plotted region of the matrix, a plot must be displayed to access these menu items. For very large matrices, you may not always want to take the time to plot the actual data. The View/Plottype/Null menu item solves this problem by displaying the current plot limits, to satisfy the program's need for a current plot without actually scanning the matrix contents. This action is very fast and is most often used before peak-picking a very large matrix, once you are confident of the settings (e.g., contour level).
After you create an intensity or contour plot of your 3D data (View/Plottype/3D Intensity or View/Plottype/3D Contour) (which can be a sub-cube of 4D data), you may want to rotate, expand, translate, or scale the plot in real time to examine the data. FELIX lets you perform these and other operations with the View/Plottype/Interactive (<Alt>-vte) menu item.
When you select this menu item, the 3D real-time control panel appears and displays the plot in the current frame. Once you select the desired real-time operation using the buttons in the panel, you apply it by moving the cursor over the plot and dragging the cursor either horizontally or vertically. You can also click with the middle mouse button and then release - the movement of the mouse is tracked until you click with the left mouse button. Downward and leftward motions decrease the values for the selected operation, and upward and rightward motions increase the values. As you move the cursor, the plot is continuously updated to show the plot after application of the selected operations.
The smoothness and speed of the real-time display are directly affected by the number of line segments in the current plot. An expanded region with a small number of contours and peak footprints rotates very smoothly, but a full plot with many contours may flicker as it rotates.
The real-time operations and their effects on the rendering of the plot are listed in Table 4. The x- and y-axes lie parallel to the monitor screen surface, and the z-axis runs perpendicular to the screen.
In addition to the standard plot types for ND data, FELIX can make 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 features that are far apart in the actual matrix to be displayed on a single plot. A special tile plot in which one of the axes runs across the full spectrum is a strip plot. These types of plot can be turned on and off using the View/Plottype/Tile/Strip Plot toggle.
The items in the Limits menu provide numerous options for quickly changing the expansion limits.
The View/Limits/Set Limits menu item (<Alt>-vls or <Ctrl>-s) lets you choose the spectral limits in real time. When you select this menu item, a spot pointer appears. Move this pointer 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.
Use View/Limits/Manual Limits menu item (<Alt>-vlm) when you have specific values for the limits and want to expand the plot to those precise 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.
The View/Limits/Full Limits menu item (<Alt>-vlf or <Ctrl>-f) restores the full spectrum display.
The View/Limits/Last Limits menu item (<Alt>-vll) redisplays the plot with the previous limits. With this menu item you can rapidly restore an expanded plot.
To exchange the current horizontal plot limits with the current vertical plot limits, select the View/Limits/Transpose Limits (<Alt>-vlt>) menu item. This switches the limits and redraws the plot and 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.
The View/Limits/Order of Plot (<Alt>-vld) menu item lets you 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 menu item, a control panel prompts you to choose the plot order. For a 2D matrix the toggle has two possible states: D1 - D2 specifies that the plot be ordered with D1 along the x axis and D2 along the y-axis; and D2 - D1 specifies that the plot be ordered with D2 along the x axis and D1 along the y axis. For a 3D or 4D matrix you can explicitly specify what the order should be - a control panel prompts you for the dimension numbers that you want displayed along the x, y, and z-axes.
If you have displayed a 2D, 3D, or 4D matrix you can select 1D vectors using the following set of menu items.
The View/Limits/1D Horizontal (<Alt>-vlr) menu item lets you 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.
The View/Limits/1D Vertical (<Alt>-vli) menu item 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 display. The plottype popup on the iconbar changes to 1D.
The View/Limits/1D Orthogonal (<Alt>-vlg) menu item 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 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 a4D spectrum the slice runs along the third (order3) dimension.
The View/Limits/1D Orthogonal 2 (<Alt>-vln) menu item 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. 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.
If you have displayed a 3D or 4D matrix you can select 2D planes for viewing using the following set of menu items.
The View/Limits/Real-time Plane (<Alt>-vl-) menu item brings up the plane-selection slider and lets you view a 2D plane from a 3D or 4D spectrum.
By using the View/Limits/Select Plane (<Alt>-vlp) menu item you can specify a 2D plane for display. A control panel prompts you for the matrix slice. Selecting the switch beside the plane that interests you. entering the value of the point or ppm value for the specific plane in the corresponding box, setting whether ppm or point should be used, then selecting OK causes FELIX to display the requested 2D slice.
The View/Limits/Horizontal Plane (<Alt>-vlh) menu item 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 menu item causes 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 menu item appears as Horizontal Plane (D1-D3).
For a 4D matrix, an additional menu item (View/Limits/Horizontal 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 Horizontal Plane (D1-D3) and a Horizontal 2 Plane (D1-D4) menu item are available).
The View/Limits/Vertical Plane (<Alt>-vlv) menu item 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 menu item causes FELIX to display a vertical line cursor. Clicking the desired line on the currently-displayed 2D slice causes FELIX 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 menu item appears as Vertical Plane (D2-D3).
For a 4D matrix, an additional menu item (View/Limits/Vertical 2 Plane (<Alt>-vl2)) enables you to select along the other orthogonal direction (for example, if your current display is D1-D2, then both a Vertical Plane (D2-D3) and a Vertical 2 Plane (D2-D4) menu item are available).
The View/Limits/Orthogonal Plane (<Alt>-vlo) menu item lets you use a cursor to select a slice that is orthogonal relative to the current 2D slice of a 4D matrix. Selecting this menu item causes FELIX to display 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 menu item appears as Orthogonal Plane (D3-D4).
You can redefine limits in the current frame as with the previous View/Limits menu items, and you can also define new limits in another frame using the View/Export Limits (<Alt>-ve) menu items, as described below.
The View/Export Limits/Export 1D Horizontal (<Alt>-ver) menu item 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.
The View/Export Limits/Export 1D Vertical (<Alt>-vei) menu item 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.
The View/Export Limits/Export 1D Orthogonal (<Alt>-veg) menu item 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.
The View/Export Limits/Export 1D Orthogonal 2 (<Alt>-ven) menu item 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.
The View/Export Limits/Export 1D Transposed (<Alt>-vet) menu item 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.
If you have displayed a 3D or 4D matrix, you can export 2D planes to a different frame using the following set of menu items.
The View/Export Limits/Export Limits (<Alt>-vee) menu item allows you to export the plot limits from the current frame to another frame.
The View/Export Limits/Export Horizontal (<Alt>-veh) menu item 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 menu item causes 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 menu item appears as Export Horizontal (D1-D3).
For a 4D matrix there is an additional menu item (View/Export Limits/Export Horizontal 2 (<Alt>-vez)), which allows you to select along the other orthogonal direction (for example, if your current display is D1-D2, both a Export Horizontal (D1-D3) and a Export Horizontal 2 (D1-D4) menu item are available).
The View/Export Limits/Export Vertical (<Alt>-vev) menu item 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 menu item causes FELIX to display a vertical line cursor. Clicking the desired line on the currently displayed 2D slice causes 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 menu item appears as Export Vertical (D2-D3).
For a 4D matrix there is an additional menu item (View/Export Limits/Export Vertical 2 (<Alt>-ve2)), which allows you to select along the other orthogonal direction (for example, if your current display is D1-D2, both a Export Vertical (D2-D3) and a Export Vertical 2 (D2-D4) menu item are available).
The View/Export Limits/Export Orthogonal (<Alt>-veo) menu item lets you use a cursor to select a slice that is orthogonal relative to the current 2D slice of a 4D matrix. Selecting this menu item causes 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 menu item appears as Export Orthogonal (D3-D4).
The View/Export Limits/Export Transposed (<Alt>-ved) menu item lets you use a cursor to select a slice that is transposed relative to the current 2D slice of a 3D matrix. Selecting this menu item causes FELIX to display a crosshair cursor. Clicking the desired spot on the currently displayed 2D slice causes FELIX to load 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 already exist.
The View/Draw Peaks (<Alt>-vd or <Ctrl>-k) menu item displays 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 menu item. Setting the toggle on causes the peaks to display after every spectrum plot.
The View/Draw Frequencies (<Alt>-vf) menu item displays 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 menu item. Setting the toggle on displays the frequencies after every spectrum plot.
The View/Draw Integrals (<Alt>-vs) menu item displays the integrals on a 1D spectrum, according to the parameters specified using the Preference/Integral menu item. Setting the toggle on displays the integrals after every 1D plot.
The View/Draw Basepoints (<Alt>-vb) menu item displays the picked baseline points on a 1D spectrum. Setting the toggle on displays the points after every spectrum plot.
The View/Draw Annotations (<Alt>-va) menu item displays the annotations in the current annotation file (annfil). Setting the toggle on displays the annotations after every spectrum plot.
The View/Draw 1D Slices (<Alt>-v1) menu item specifies 1D sections to export to a different frame (or frames) interactively using the cursor from the current matrix. If the setup has not been done yet (Preference/ 1D Slice), you are asked to specify which dimension(s) to take the 1D slices from. A line is drawn on the parent plot showing the location from which the slice was extracted.
The View/Multiple 1D Slices (<Alt>-vm) menu item specifies multiple 1D sections to export to a different frame (or frames) interactively, using the cursors drawn on top of each other in a stack. If the setup has not been done yet (Preference/ 1D Slice), you are asked to specify which dimension(s) to take the 1D slices from. A line is drawn on the parent plot showing the location from which the slice was extracted.
The View/Thick 1D Slice (<Alt>-vk) menu item specifies a thick 1D section (the result of co-addition of multiple rows) to export to a different frame (or frames) interactively, using the cursor from the current matrix. If the setup has not been done yet (Preference/ 1D Slice), you are asked to specify which dimension(s) to take the 1D slices from.
The View/Draw 2D Slices (<Alt>-v2) menu item specifies 2D sections to export from the current 3D or 4D matrix to a different frame (or frames) interactively, using the cursor. If the setup has not been done yet (Preference/ 2D Slice), you are asked to specify which dimension(s) to take the 2D slices from. A line is drawn on the parent plot showing the location from which the slice was extracted.
Tile plots appear 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. In this manner, the unit of interest is always a line segment, or region, in a single dimension; while the tile plot is simply the display of the intersections of these segments. A 2D cross-peak footprint can also be thought of as the intersection of two line segments.
Tiles are always stored 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 make a tile plot, FELIX reads the tile entity to determine which regions to tile.
The View/Tile Plot (<Alt>-vi) menu item brings up a pullright menu of tile controls, which are described below.
The View/Tile Plot/Tile Plot menu item (<Alt>-vie) toggles the tile plot on or off (after a tile entity is defined with, for example, the Tile One Peak or Tile Regions menu item).
The View/Tile Plot/Tile One Peak (<Alt>-vip) menu item creates 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, and the peak entity is searched 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. Alignment criteria are set with the View/Tile Plot/Tile Plot Parameters menu item.
The View/Tile Plot/Tile Regions (<Alt>-vir) menu item creates a tile entity and plot from a user-generated set of regions. The action supplies a small crosshair cursor with which to select a rectangular region. Each such region defines up to two line segments for the tile entity. You can drag out additional regions to define more segments. Click outside the plot to quit selecting regions. The resulting tile plot shows all the regions in the matrix where these segments intersect. Segments that are almost identical (those with significant overlap) are combined.
This menu item can be used only in conjunction with Assign. Here you can define a tile plot using any combination of frequency clipboards, protopatterns, and patterns.
A tile plot may have too many line segments, so that the display shows regions that are not of interest. The View/Tile Plot/Delete One Column (<Alt>-vio) and View/Tile Plot/Delete One Row (<Alt>-vid) menu items let you manually remove a single line segment from the entity to generate a new tile plot with fewer tiles. A half-crosshair cursor allows you to graphically delete a line segment from the entity. The new reduced tile plot is then displayed.
The View/Tile Plot/Tile Plot Parameters (<Alt>-vit) menu item opens a control panel that affects many facets of tile plot creation and display. You can set the name of the tile entity, the explicit width for all peak-based line segments, the behavior for treatment of overlapping line segments, and the criteria for determining cross-peak alignment. Specifically, 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.
The View/Strip Plot/Strip Plot menu item (<Alt>-vrr) changes a strip plot to a regular plot or turns on a previously defined strip plot from a regular plot.
The View/Strip Plot/Strip Plot of Clipboard menu item (<Alt>-vrc) generates a strip plot representation from the current frequencies in the clipboard.
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.
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).
The View/Strip Plot/Make One Horizontal Strip menu item (<Alt>-vrh) quickly generates 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.
The View/Strip Plot/Make One Vertical Strip menu item (<Alt>-vrv) quickly generates 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.
The View/Strip Plot/Make One Orthogonal Strip menu item (<Alt>-vro) draws 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. The plot is zoomed according to the starting and ending position of the cursor. The long axis of the strip plot will be the current orthogonal dimension.
If the strip plots are too thin, you can correct them by redefining the scaling with the View/Strip Plot/Scale Strip Plot menu item (<Alt>-vrs).
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.
The items in this pulldown allow you to view and edit entities in spreadsheet tables, delete entities, and add annotations to spectra.
The Edit/Table menu item (<Alt>-et) opens any existing entity from the database in the spreadsheet viewer. You should select the entity with the entity-selection tool.
The Edit/Peaks menu item (<Alt>-ek) opens 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 and 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 menu item and icons to streamline navigation in the spectrum and interaction with the peaks.
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.
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.
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.
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.
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.
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.
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.
The Edit/Table Delete menu item (<Alt>-ed) deletes an entity (or table) from the database. You need to select the entity with the entity-selection tool. Closing the spreadsheet view of an entity does not remove that entity from the database. To achieve this, you need to delete it through this menu item.
Annotations can be added 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, an entirely new annotation file must be created or the old one must be edited to obtain the desired placement of these items.
To activate the annotation interface, select the Edit/Annotation menu item (<Alt>-ea). In the resulting control panel, you can perform one of these five operations:
When either the Build or Append button is selected, an new menu of annotation functions (detailed below) appears. You may then add, move, and delete various annotations. To exit the annotation interface and save your file, select Exit at the bottom of the Annotations menu. Short descriptions of items in the Annotations menu are given below.