Displaying a FID or 1D Spectrum
Click the Display FID graphics control button to display a FID. Click the 1D Spectrum graphics control button to display a 1 D spectrum.

FID Display
After data is acquired, a FID becomes available for displaying. Clicking the FID button on the graphics control bar displays a FID and enables interactive manipulation of the FID display. The FID display graphics buttons change to show that multiple FIDs can be viewed. The FID is left shifted by the number of complex data points specified in the Left Shift FID field on the Linear Prediction page.

Spectrum Display
After data is transformed, a spectrum becomes available for display and plotting. The normal spectrum display enables interactive manipulation of a single 1D spectrum. A spectrum is displayed by clicking the 1D Spectrum graphics control button or by transforming a data set.

Interactive Display Tools

Mouse buttons The mouse button correspond to the display parameters shown on the lower right part of the graphics window. These display parameter change as you select the different graphics control functions. Typically, the left button controls the left cursor position, the middle button controls vertical scaling, and the right button controls the right cursor or delta between the two cursors.
Graphics control buttons
The graphics control bar is arranged vertically to the left of the graphics canvas. The graphics control buttons provide controls for cursors, zooming, scales, grab & move, threshold, phasing, and refresh. Different functions appear for FID or spectrum display.

The Display page on the Process tab provides appropriate display parameters, including display mode, axis, and amplitude scaling. The Display menu provides tools for displaying multiple spectra, plotting, and creating insets.

A typical use of these tools might be expanding a region on a spectrum:
1. Display the spectrum -- click the spectrum icon on the graphics control bar.
2. Select the region to expand -- left click on the spectrum to place the cursor on the left boundary of the region of interest, and right click to designate the right boundary. Use the left mouse button to drag the left cursor and right button to drag the right cursor until the region you want to expand is between the cursors.
3. Expand the region -- click the magnifying glass icon on the graphics control bar.

Controlling Cursors and Vertical Scale
Click the mouse buttons in the graphics display window to position cursors and adjust the FID or spectral vertical scale and position.
Display Limits
The Screen Position buttons (Full, Enter, Left, Right) on the Display page place the display and plot in the desired portion of the page. The wysiwyg parameter is useful for scaling the image to a full window instead of the same size as the plot. This parameter is set in the Edit -> System settings window, on the
Display/Plot tab.
Set display from plotter aspect ratio (wysiwyg)
Graphics Control Buttons
Use the Graphics control buttons in combination with the mouse buttons for complete interactive control of the displayed FID or spectrum.
• FID Display Buttons
• 1D Spectrum Display Buttons
Left cursor -- Click the left mouse button to position the cursor and update the value displayed for the crf or cr parameter (crf for a FID or cr for a spectrum). Right cursor (box) -- Click the right mouse button to display and position a second cursor to the right of the original cursor. The value of the parameter deltaf for a FID or delta for a spectra changes with the position of the right cursor and is the difference in seconds between the two cursors. Two cursors -- If both cursors are displayed, the left mouse button moves both cursors simultaneously, leaving the distance between them (deltaf or delta) unchanged. Vertical scale --Click the middle mouse button to adjust the vertical scale of the FID (vf parameter) or spectrum (vs parameter). Vertical position -- To adjust the vertical position of the FID, click and hold the middle mouse button near the left edge of the graphics display and slide the FID or spectrum up or down. The value of vpf or vp (or vpfi if the imaginary channel) is will change.

Display Limits
The Screen Position buttons (Full, Enter, Left, Right) on the Display page place the display and plot in the desired portion of the page. The wysiwyg parameter is useful for scaling the image to a full window instead of the same size as the plot. This parameter is set in the Edit -> System settings window, on the
Display/Plot tab. Set display from plotter aspect ratio (wysiwyg)

Checked scales the image to the current plotter setting (wysiwyg). Unchecked scales the image to the full window, which is easier to view. This option scales the window but does not change the ratio of the image.

Spectrum Display Buttons
Clicking the spectrum button on the graphics control bar displays a spectrum and enablesinteractive manipulation of the FID. To the left of the display is the spectral display graphics control buttons (note that the labels change on some of the buttons according to the mode of the program):

These buttons function as follows:
Cursor or Box

Box --Change to the box mode with two cursors.

Cursor --Change to the cursor mode with one cursor.

Expand or full display

Expand --Expand the area between the cursors.
Full --Display the full area.

Set integrals --The first click displays the intregal function buttons. The second click displays the No Integral and Clear Resets buttons.
Full integral -- Display all integral regions.
Integral resets -- Open an interactive integral reset mode. The left mouse button defines an integral reset at the current mouse position. The right mouse button removes an integral reset closest to the current mouse position. The middle mouse button adjusts the scale. The integral does not have to be displayed. However, if the integral is displayed in the “partial” mode, the normally blanked regions are displayed as dotted lines. To clear the integral reset points before beginning, click the Clear Resets button.
Integral Lvl/Tlt Open interactive zero- and first-order baseline correction mode.
Scale -- Display a time scale under the spectrum in units specified on the Display page.
Grab and Move -- Opens the interactive spectral windowing mode. Use the left mouse button to adjust the starting time of the display and move the display left or right. Use the right mouse button to adjust the width of the display.

Threshold -- Toggles the display of a horizontal cursor. The left mouse button positions this cursor at the mouse arrow position. The middle mouse button adjusts the scale.
Phase -- Opens the interactive phasing mode. Use the left mouse button for courseadjustments (180°) and right button for fine adjustments (20°), where full scale corresponds to 180°. Use the middle button
to adjust the vertical scale of the display and to apply the latest phase correction to the entire spectrum.
Refresh -- Open an interactive integral reset mode.
Return -- Returns to the last menu.

Line Tools
VnmrJ provides tools for finding the nearest line, measuring line resolution, and displaying line lists.
• Find Nearest Line and Line Resolution
• Display Line List
Find Nearest Line and Line Resolution
1. Place a cursor near the line of interest.
2. Select the Process page and click the Find nearest line button. The cursor moves to the nearest line and displays its height and frequency (in Hz and ppm) in the message window.
3. Click Display linewidth to display the resolution of a line, as well as the limiting digital resolution of the spectrum.The resolution is determined by a width at halfheight algorithm and not by least-squares.
Display Line List
1. Click the Threshold graphics control button and use the middle mouse button to vertically position the yellow threshold line.
2. Select the Line List page and click the Display Line List button. This processdisplays line frequencies and intensities that are above a threshold.

Spectral Referencing
Frequency referencing is set on the Display page.
Terms used in spectral referencing:
The By Solvent and By TMS buttons assume that the system is locked (and that the lock solvent is defined in /vnmr/solvents). If you are working without lock and still want to use these buttons, you must ensure that the field offset has been adjusted so that the lock frequency is on resonance with a sample of similar susceptibility. To ensure that the field offset is adjusted, do the following procedure:
1. Insert a sample with deuterated solvent.
By Solvent Reference the spectrum to a selected solvent line. Use the Find nearest line button on the Process page to place the cursor.By TMS Reference the spectrum to a TMS line. In the case of other signals (e.g., from silicon grease) immediately to the left of the TMS line (even if they are higher than the reference line), tmsref tries avoiding those signals by taking the line furthest to the right in that area, as long as it is at least 10% of the main Si-CH₃ signal. Large signals within 0.6 ppm for ¹H (or 6 ppm for ¹³C) to the right of TMS might lead to misreferencing. Cancel Clears the reference line by removing any spectral referencing present, and turns off referencing. By Cursor References the spectrum based on the current cursor position. If you want to reference the spectrum based on a line position in the spectrum, first use the Find nearest line button on the Process page, then click By Cursor. Reference line The distance, in Hz, of the reference line from the right edge of the spectral window. This line is the spectral position used to set the referencing. It can be the signal of a frequency standard (such as TMS), or any line (such as a solvent signal) with a known chemical shift (in ppm), or a position in the spectrum where you expect such a line to appear.
Reference position The difference between the reference line and the reference frequency (zero position of the scale), in Hz. If you referencea spectrum using the signal of a frequency standard, such as TMS, then reference position is 0. The distance of the reference frequency from the right edge of the spectrum is
reference line - reference position. Spectrometer frequency The absolute frequency, in MHz, of the center of the spectrum (the transmitter position). In order to see the accurate value of the spectrometer frequency (sfrq parameter), you should use the spcfrq command. Reference frequency The frequency, in MHz, of the frequency standard, i.e., the zero position of the frequency scale, and the divider (unit) for the calculation of ppm scales.

The By Solvent and By TMS buttons assume that the system is locked (and that the lock solvent is defined in /vnmr/solvents). If you are working without lock and still want to use these buttons, you must ensure that the field offset has been adjusted so that the lock frequency is on resonance with a sample of similar susceptibility. To ensure that the field offset is adjusted, do the following procedure:
1. Insert a sample with deuterated solvent. By Solvent Reference the spectrum to a selected solvent line. Use the Find nearest line button on the Process page to place the cursor. By TMS Reference the spectrum to a TMS line. In the case of other signals (e.g., from silicon grease) immediately to the left of the TMS line (even if they are higher than the reference line), tmsref tries avoiding those signals by taking the line furthest to the right in that area, as long as it is at least 10% of the main Si-CH3 signal. Large signals within 0.6 ppm for 1H (or 6 ppm for 13C) to the right of TMS might lead to misreferencing. Cancel Clears the reference line by removing any spectral referencing present, and turns off referencing. By Cursor References the spectrum based on the current cursor position. If you want to reference the spectrum based on a line position in the spectrum, first use the Find nearest line button on the Process page, then click By Cursor. Reference line The distance, in Hz, of the reference line from the right edge of the spectral window. This line is the spectral position used to set the referencing. It can be the signal of a frequency
standard (such as TMS), or any line (such as a solvent signal) with a known chemical shift (in ppm), or a position in the spectrum where you expect such a line to appear. Reference position The difference between the reference line and the reference frequency (zero position of the scale), in Hz. If you reference
a spectrum using the signal of a frequency standard, such as TMS, then reference position is 0. The distance of the reference frequency from the right edge of the spectrum is reference line - reference position. Spectrometer frequency The absolute frequency, in MHz, of the center of the spectrum (the transmitter position). In order to see the accurate value of the spectrometer frequency (sfrq parameter), you should use the spcfrq command. Reference frequency The frequency, in MHz, of the frequency standard, i.e., the
zero position of the frequency scale, and the divider (unit) for the calculation of ppm scales.
Displaying FIDs and Spectra
1. VnmrJ Liquids NMR 2. Adjust z0 (or lkof) in acqi so that the lock frequency is on resonance.
3. Switch off the lock.
4. Insert the nondeuterated sample.
The accuracy of the solvent and TMS referencing buttons is mostly limited by the accuracy
of the chemical shift of the lock resonance line, which may depend on the concentration
and the chemical properties (acidity/basicity) of the components in the sample. But they
should normally be accurate enough to find an actual reference line close to its predicted
position.
Estimating the position if the reference frequency in spectra from unlocked samples,
provided the spectrometer is first locked on a sample with similar susceptibility, then the
lock is disengaged and the field offset adjusted such that the lock signal is on-resonance.
Now, you can acquire spectra without lock and calculate their (estimated) referencing using
setref, provided the solvent parameter is set to the solvent that was last locked on.

Integration

1. Left click on an integral region of interest, about halfway vertically up the screen. A horizontal cursor intersects at the mouse arrow. Two vertical cursors are placed on either side of the mouse arrow.
2. Right or left click above or below the horizontal cursor, but within the two vertical cursors, to adjust the zero-order baseline correction parameter lvl.
• Clicking the above the horizontal cursor increases lvl.
• Clicking below the horizontal cursor decreases lvl.
• Clicking on the horizontal cursor restores the initial baseline correction value.
3. Left click on another region of the spectrum, outside the vertical cursors.
A new horizontal cursor displays at the mouse arrow, two new vertical cursors display on either side of the mouse arrow, and a single vertical cursor displays in the middle of the region where lvl was being updated. The mouse now controls the first-order baseline correction parameter tlt.
4. Right or left click above or below the horizontal cursor to increase or decrease tlt, and change lvl so that the total drift correction at the single vertical cursor in the middle of the previous region is held constant.
This process eliminates or substantially reduces the necessity to iteratively adjust the two parameters lvl and tlt. As with the zero-order correction, placing the mouse arrow right on the horizontal cursor and clicking the mouse button will restore the initial baseline correction values. Each time the mouse is clicked outside the two vertical cursors, new vertical and horizontal cursors display. The left and right mouse buttons both adjust the baseline correction parameters and differ only in their sensitivity. The left button causes changes a factor of eight times larger than the right button, and hence you can consider the left button the “coarse” adjust and the right button the “fine” adjust. The overall sensitivity of these
adjustments can also be controlled by the parameter lvltlt. This parameter is a multiplier, with a default value of 1.0, for the size of the changes. To make larger changes, make lvltlt larger than 1.0. To have finer control, set lvltlt to be between 0.0 and 1.0. The middle mouse button adjusts the integral scale (parameter is) or the integral offset (parameter io), exactly as whenever an integral is displayed.
5. Exit the interactive baseline correction mode by clicking on another graphics control button.
Displaying Integrals Step-by-Step

The following methods should give you an opportunity to compare procedures. Before starting each procedure, be sure to obtain a typical spectrum or by entering:
1. Click the magnifying glass button on the Locator.
2. Select Sort by Directory.
3. Drag fid1d to the graphics window.
4. Transform the data if necessary.
Integration Fully Automated Method
1. Click on AutoRegion.
The integral display mode is changed so that only every other integral region is displayed, and the spectrum is automatically broken into integral regions.
2. Select the Display page and click on the bc button. A spline-fit baseline correction is performed (by the command bc) to produce the flattest possible baseline.
3. Select the Cursors/Integration page and click on the Scale to Fit button (the command isadj). The largest integral is adjusted to a reasonable size.
4. Select the Line Lists page and click on the Display List of Integrals button (the command dli). The text window displays a list of integral intensities.
Manual Method

1. Click on Clear Integrals or use click on the Set Integrals icon. Any currently defined integral reset points are cleared.
2. Click on the Second Integral icon. The integral display mode is changed so that only every other integral region is displayed.
3. Click the left button slightly to the left of the left-most group of peaks. This establishes the end of the first (from the left end) section of baseline. Position the mouse cursor anywhere vertically that seems most comfortable.
4. Click the left button slightly to the right of the left-most group of peaks. This establishes the end of the first section of peaks.
5. Repeat steps 4 and 5 for each group of peaks across the spectrum. The reset points must alternately separate baseline and peaks. If two peaks are adjacent to each other to put a reset between them, click the button twice at the same place. This establishes a “baseline” region of zero length. Note it is also possible to add additional resets in this way to resets that were established automatically by the region command.
6. Place the mouse pointer on the left side of the spectrum, press and hold the middle mouse button, and move the spectrum to make room for the display of integral values.
7. Click the center mouse button above the right end of any displayed integral. This adjusts the integral vertical scale

8. Enter a value in the normalize box you wish to assign to the sum of the integrals. The value entered affects only printed output, not the trace of the integral.
9. Select Display Normalized Integrals. The text window displays a list of integral amplitudes. The sum of the integrals isnormalized to the value of the parameter ins.

Baseline Correction
Almost all of the operations performed on spectra assume a “good” baseline. Line lists, integrations, resolution measurements, 2D volume integrations, etc., all measure intensities from “zero” and do not perform any baseline adjustments. If the baseline in your spectrum is not “good,” you should first perform a baseline correction operation before performing further data reduction. Two types of baseline correction are provided, linear and non-linear, and are available using the buttons on the Display page. The dc command turns on a linear baseline correction, using the beginning and end of the displayed spectrum to define a straight line to be used for baseline correction. The result is to calculate a zero-order baseline correction parameter lvl and a first-order baseline correction parameter tlt. The cdc command turns off this correction. The results of the dc or cdc command is stored in the dcg parameter, which can be queried (dcg?) to determine whether drift correction is active. If active, dcg=''; if inactive, dcg='cdc'. The bc command turns on 1D and 2D baseline correction. The 1D baseline correction uses spline or second to twentieth order polynomial fitting of predefined baseline regions. bc defines every other integral, that is, those integrals that disappear in partial integral mode (intmod='partial') as baseline and attempts to correct these points to zero. A variety of parameters can be used to control the effect of the bc command. For more information about the bc command, refer to the entry for bc in the Command and Parameter Reference.
Integral Reset Points
The z command (or the equivalent button or icon) resets the integral to zero at the point marked by the displayed cursor. z(reset1,reset2,...) allows the input of the reset points as part of a command, instead of using the position of the cursor. Reset points do not have to be entered in order. The resets are stored as frequencies and will not change if the parameter fn is changed. The command cz (or the equivalent button) removes all such integral resets. cz(reset1,reset2,...) clears specific integral resets. For a list of integrals, the liamp parameter stores the integral amplitudes at the integral resets points and the lifrq parameter stores the frequencies of integral reset points. To display the values of liamp, enter display('liamp') with a Text Output page selected. Frequencies are stored in Hz and are not adjusted by the reference parameters rfl and rfp.
Integral Regions
The region command divides a spectrum up into regions containing peaks. A variety of parameters can be used to control the effect of the region command; see the Command and Parameter Reference for details.
Integral Display and Plotting
Display and plotting of the integral trace is independent of the values of the integrals. The height of the trace is controlled by the parameter is and can be interactively adjusted with the ds command. Also, the macro isadj(height) (or the equivalent button) adjusts the integral height so that largest integral fits the paper or is height mm tall if an argument is provided, for example, isadj(100). The command dli (or the equivalent button) displays a list of integral values at the integral reset points. The frequency units of the reset points are defined by the parameter axis. The reset points are stored as Hz and are not referenced to rfl and rfp. The amplitudes are stored as actual values; they are not scaled. The integral values are scaled by the parameters ins and insref and the Fourier number. Typically, ins is set to the number of nuclei in a given region. For example, if a region represented a single methyl group, the following procedure would scale the integral values of that region:
1. Set ins=3.
2. Set insref to the Fourier-number-scaled-values of that integral.
3. Enter dli. The integral value of that region is displayed as 3 and all other integral values are accordingly scaled.
Integral value scaling can be interactively set with the ds command. The setint macro can also be used to adjust integral value scaling. setint sets the value of an integral and is used in conjunction with the command dli to scale integral values.Normalized integral values can also be selected. In this case, ins represents the total number of nuclei. The individual integral values will be scaled so that their sum is equal to ins. The normalized mode may be selected by setting insref to “not used.” The integral is scaled by ins and insref.
Two commands are closely related to dli:
• nli is equivalent to dli except that no screen display is produced.
• dlni normalizes the values from dli using the integral normalization scale parameter ins and then displays the list.
The dpir command displays numerical integral values below the appropriate spectral regions, using the integral blanking mode in which only every other integral is plotted. The command dpirn shows the normalized integral values in an analogous fashion. The pir command plots digital integral values below the spectrum, using the integral blanking mode in which only every other integral is plotted. The command pirn plots the normalized integral values in an analogous fashion.