1D Processing

About the lessons

In Lesson 1: Introduction to 1D processing, you learn the basics of loading and processing 1D data files.


In Lesson 2: Advanced 1D processing, you learn some of the many options available for processing 1D data.


Lesson 1: Introduction to 1D processing

This lesson introduces the FELIX novice to some of the commands FELIX uses to process a one-dimensional data set.

In this tutorial you will process an 1D NMR data set. Once you're comfortable with the procedures, this task takes approximately ten minutes to complete.

1.   Setting up for the lesson

If not done yet, set up the tutorial files as described in "Setting up tutorial files" on page viii.

The files for this lesson are located in the 1D\Lesson1 folder.

2.   Starting FELIX

By default, FELIX works within the directory where it was opened. For standard installation, this is the C:Program Files/Accelrys/Felix2004 folder. In order to have FELIX look for and create files in another directory, you need to change the current directory.

Open the Preference/Directory... command. Change the Current Working Directory to C:\Felix_Practice

Select the File/Open command. Set the File Type parameter to Other Data [Bruker, Varian...]. Next, navigate to the tutorial\1D\Lesson1\1 folder. From the contents of this folder, select the fid file. Click OK to confirm the selection. FELIX opens the file in the window.

This loads the data. The graphics frame displays a 32768 point FID, which we can now process.

Routine 1D data processing often consists of removing DC offset, multiplying the FID by an exponential window function, transforming the results into the frequency domain, and phasing the spectrum to obtain pure absorption peaks. Subsequently, baseline roll is removed and the spectrum is integrated. We will follow these steps here.

3.   Removing DC offset

Select the Process1D/DC Offset command and choose Oversample DBC as Type. Click OK to perform the DC offset removal.

FELIX calculates a value for the baseline from the last 20% of the data points and subtracts that value from each data point.

4.   Applying Window Function

Select the Process1D/Window Function command to obtain a control panel that prompts for a window function. Enter Exponential as the Window function and click OK. In the following control panel, enter 0.2 for Line Broadening and Click OK to multiply the data by an exponential window function.

The display is updated to show the results.

5.   Fourier-transforming the data

Now, transform the data from the time domain to the frequency domain using the oversampled transform (these data were collected as a Bruker oversampled spectrum).

Select the Process1D/Transform command. FELIX determines that the transform type should be Oversampled FFT. Click OK.

The result is a spectrum in the graphics frame. Notice that the spectrum requires some phase correction. This is most easily applied by first using the phase parameter values from the procs file.

Select the Process1D/Phase Correction command. Set the Method to Parameter and leave the Zero and First Order parameters at their current values (136.912 and 14.55447, respectively). Click OK.

This should produce an almost perfectly phased spectrum. If you need to adjust the phasing, you can use the real-time phase interface.

To activate the real-time phase correction interface, select the Process1D/Phase Correction command and select the Real-Time option. Since this is a modeless dialog, you can still activate the main menu and toolbar icons to adjust the display of the spectrum while the phasing dialog is on. Use the REAL TIME PHASING dialog to adjust the pivot point position, the zero-order phase correction (Phase0), and the first-order phase correction (Phase1).

Change pivot point by clicking the Pivot button and then click the desired spectral point. Change the phase values by sliding either of the sliders left or right. These changes are visible in the display as you make them.

Repeat this with each correction until you are satisfied with the spectrum, then click OK to complete the phase correction.

This removes the real-time phase interface and makes the phased spectrum appear in the graphics frame.

6.   Performing the baseline correction

Select the Process1D/Baseline Correction command. Toggle the Baseline Point to on. Leave the parameter at Auto Pick Points as is. Click OK. In the next control panel, leave the Interval Size at 128 and Maximum Deviation at 5. Click OK.

After FELIX selects the baseline points, it marks their locations with red tics at the bottom of the display frame.

In the BASELINE CORRECTION dilaog, toggle the Baseline Correction to on and select the Polynomial option. When the dilaog appears that prompts for the Polynomial order, click OK to select the default of 5 (fifth-order polynomial).

FELIX applies the polynomial function to the spectrum.

In the BASELINE CORRECTION dialog, click Done to close it.

7.   Integrating and displaying the data

The last step is to integrate the areas of the peaks and display the integrals as a cumulative sum.

Select the View/Draw Integrals command.

FELIX calculates the integral of the peaks and displays the integral on the spectrum.

Note: This integrates the whole spectrum. For more sophisticated integration, you can use the Measure/Integral or Volume command.

8.   Exiting FELIX

To exit FELIX, select File/Exit to begin the shutdown sequence. You either leave the Save Current Session and Save Current Database parameters on; or, toggle them to off. Then click OK.

This shuts down FELIX. If you choose to save the current session and save the current database, all of the following are saved: the current session and the baseline points or integrals in the database file you selected when the program started.

After this brief tour, you should be familiar with the basic 1D processing features of FELIX and how to navigate through the menu system.

Lesson 2: Advanced 1D processing

In this tutorial you read in a file of raw NMR data, process it to obtain a spectrum of resonances (peaks), and change the spectrum's display and annotations. This takes approximately 20 minutes to complete once you are comfortable with the procedures.

1.   Setting up

If not done yet, set up the tutorial files as described in "Setting up tutorial files" on page viii.

Locate the files listed below in the 1D\Lesson2 folder.

2.   Starting FELIX

Start FELIX by double clicking the Felix icon on your desktop, or by clicking the Start button on the Windows taskbar, then selecting Programs/Accelrys/Felix 2004/Felix 2004.

If FELIX prompts you to restore from last session, click Cancel.

3.   Selecting a database

The database is a binary file where FELIX stores data like segments, baseline points, peaks, volumes, etc. The Edit/Table command gives you access to all data stored in the database. The File/Export/Table and File/Import/Table commands allow you to read and write the data as ASCII files.

Open the Preference/Directory... command and navigate the Current Working Directory to C:\Felix_Practice\1D\Lesson2\. Start working with a new database using the File/New command, selecting the option to Create a new matrix or DBA file. Make sure the File Type is set to DBA(*.dba) and enter test2 into the File Name field. Click OK.

Where you create or open the .dba file will determine your initial working directory. You can always change the working folder by selecting Preference/Directory.

4.   Reading the data file

Now you proceed to manipulate files and workspaces.

Select the File/Open command. Set the following parameter values in the dialog box:

Filename sample.dat
File Type Felix New Data
Dimension 1D

Click OK

An FID (free induction decay; the raw NMR signal) appears in the frame. This is a Bruker file and must be processed accordingly.

The following steps will show you how to open and arrange multiple spectral windows (frames) in FELIX. You can ignore them and go directly to Step 6 if you like.

5.   Creating multiple frames

Select the Window/New Layout command. Select 4 Small Square Frames.

FELIX close the original window and displays four small windows, the last one being the active one.

Now select the View/Plot command.

FELIX plots the FID in frame 4 (the active window).

Activate Frame 1 by clicking its header. Select the File/Open command. Enter sample2.dat as the Filename and click OK.

FELIX displays a different FID in the active frame.

6.   Creating additional frames

Create a new frame by selecting Window/Add New.

FELIX displays a fifth frame. All frames are automatically arranged.

Note: By default, FELIX automatically rearranges all spectral and table frames whenever a new frame is displayed. To turn off this feature, select Preference/Frame Layout and set Option to None.


To close Frame 5, click the Close Window button [X] in the upper right corner of the frame.

7.   Returning to a single frame and reading the FID

Select the Window/New Layout command and choose the 1 Frame option. This returns the screen to a single frame. Select File/Open to read in the sample.dat file as described in Step 4 above.

The above steps demonstrated how to open and arrange single or multiple spectral windows within FELIX.

8.   Processing the data to create a spectrum

Select the Process1D/DC Offset command. Set the following parameter values in the control panel that appears:

Type BC
Baseline Correct Fraction

Click OK.

Now select the Process1D/Zero Fill command and set these values:

Zerofill To 16384

Click OK.

Baseline correction corrects for the DC offset in a spectrometer. Zero filling adds zeros to the end of the FID. The default is twice as many points as the FID. The size of the FID is increased to this number of points.

Warning: If you execute this, beware that you have increased the size of your FID and resultant spectra. If you pop this to a buffer and then read in an 8K file, the buffer is also cut in half, and you lose half of your zero-filled spectra or FID!

9.   Applying a window function

Select the Process1D/Window Function command. In the control panel, choose Exponential and click OK.

In the subsequent control panel set Method to Real-Time.

FELIX displays a new modeless dilaog that allows you to adjust the windowing function interactively. The mathematical function is drawn over the FID in red. Use the slider to change the parameters for the displayed window function and the effect on the FID.

Use the slider to set the Line Broadening parameter to a value of approximately 1.1.

Click Keep.

The FID is now multiplied with the window function and you see the results.

10.   Transforming the data

Select the Process1D/Transform command. Select the Bruker FFT option.

Important: Data collected from some Bruker instruments is stored differently than data from other instruments. Hence, a special transform is needed

The Fourier transform produces the NMR spectrum.

Note: Newer versions of Bruker instruments can store data in a "normal" way. This is referred as "qsim" in the Bruker nomenclature. If a spectrum was recorded using this "qsim" parameter you must use the Real FFT command in FELIX

11.   Phasing the spectrum

Select the Process1D/Phase Correction command. In the control panel set the Method to Real-Time. Click OK.

This is an interactive phasing mode. FELIX displays a modeless dialog box with sliders and buttons. You can activate the main menu items or the toolbar icons to change the spectral display.

Set the pivot for the spectrum by clicking the Pivot button under in the dialog and then clicking the cursor where you want the pivot point to be. Drag the upper slider until the peaks around the pivot point are properly phased.

12.   Phasing an expanded region

Click the Zoom icon in the toolbar. Click-press-drag so that a rubber-band box covers the spectral region you want to zoom into. Release the button, and the selected region fills the window. Continue adjusting the Phase0 and Phase1 sliders to phase the spectrum. If necessary, click the Coarse or Fine button to increase or decrease the adjusting range, respectively.

Click the Full plot icon in the toolbar to view the entire spectrum. Click the Increase threshold icon to zoom in the y axis if necessary. When satisfied with the phasing, click the OK button.

13.   Baseline-correcting the spectrum to eliminate the curved baseline

Select the Process1D/Baseline Correction command. Toggle the Baseline Point to on and choose the Auto Pick Points option. Click OK.

Click OK in the next dialog box.

This generates a set of baseline points displayed as small red lines under the spectrum to be used in the correction.

14.   Adding user-defined base points

In the same dialog, select the Pick Points Via Cursor option. Click OK.

Next, move the vertical cursor to a point on the baseline that is not already selected with a red line, and click. This adds that point to the baseline. Repeat this process until you have defined all the desired baseline points. To quit the vertical cursor, press the <Esc> key.

15.   Viewing the base points

Click the Done button to close the BASELINE CORRECTION dialog. Select the Edit/Table command. Double-click the bas directory and then double-click the baseline table.

FELIX displays a new window with a spreadsheet. You may scroll through the selected baseline points.

Note: When one or more table windows are open, only the menu and tool bar of the currently activated window are visible. If you want to select a certain menu item or tool bar icon, be sure to click the corresponding window first to activate its menu and tool bar (if any).

16.   Applying the baseline correction

Close the table window by selecting File/Close from its own menu.

Select the Process1D/Baseline Correction command in the main menu. In the control panel, check Baseline Correction and select Polynomial. Click OK to apply the correction to the selected basepoints.

When the BASELINE CORRECTION dialog box displays again, click Done to close it.

Note: For finer adjustment of the polynomial used for baseline correction you may use the real-time Polynomial command. Here you may change the polynomial's parameters using the mouse and dial boxes. The display's appearance reflects the order of polynomial. You can change the polynomial parameters, up to the order of nine.

17.   Using real-time sliders to compare two different spectra

Select the Tools/Buffers/Store Work to Buffer command. Set the Buffer Number to 1 and click OK.

This saves the data in the workspace to the first buffer. The data in the buffers are not displayed by default. The following step will force FELIX to display the first buffer.

Select the Preference/Plot Parameters command. In the dialog box, set Stack Depth to 1. Set Color Scheme to Define. Set Color Cycle to 2. Click OK.

Two identical 1D spectra are displayed in different colors. The upper is the data in the first buffer and the lower is those in the workspace

Generally, when you open a data file or do data processing, the original data in the workspace gets overwritten. If you want to keep the original data, you must save them in a buffer before opening a new file. By default, you have up to five buffers with the same size as the workspace. You can change the number and size of the buffers using the Preference/ Memory command.

Click the Plot Parameters icon and set Stack Depth to 0. This forces that only the data in the workspace is displayed.

Read the 1D file sample.dat into the workspace as in Step 4. Apply zero filling and a different window function, e.g., Sinebell^2, using 16384 and 90.0 for parameters.

Transform the FID (Bruker FFT) and use the Process1D/Phase Correction command with the Parameter option to apply the phase correction.

Finally, select Process1D/Baseline Correction, check Baseline Correction and choose Polynomial. Click OK. When the dialog box comes up again, click Done to close it.

Since the symbols (phase0 and phase1) and database entity (bas:baseline) that save the phasing parameters have not been overwritten, the same parameters and base points are applied to both spectra.

Click the Plot Parameters icon and set Stack Depth to 1. This forces that the two data sets in the workspace and the first buffer are displayed.

Select the Preference/1D Scale command. Set Scaling to Absolute. To put the red spectrum on top of the white one, move the Overlap slider and set it to 1.0. The difference between the two should be noticeable.

Click OK to leave the real-time sliders.

18.   Getting the difference between two spectra

Select the Tools/Buffers Subtract from Buffer command. Set the Buffer Number to 1, then click OK.

This subtracts the data in buffer1 by those saved in the workspace. The difference spectrum is displayed as buffer 1. The data in the workspace remain unchanged.

Select the Preference/Plot Parameters command. In the dialog box, set the Stack Depth to 0, then click OK.

This displays only the spectrum in the workspace.

19.   Viewing an expanded region

Click Zoom. Click and hold the left mouse button and drag the mouse so that the rubber box covers the region around the water resonance (~7000-9000 points). Release the left mouse button.

20.   Setting the reference on water peak

Select the Preference/Reference command. Click the Cursor button, and the cursor becomes a vertical line. Now click the water resonance (at ~8200 points). FELIX displays the control panel again. From the Axis Type popup select the Ppm option. Set Reference PPM to 4.76 and click OK.

FELIX redisplays the spectrum with new ppm units.

Click the Full Plot icon in the toolbar. Or, you may press <Ctrl>+f on the keyboard.

21.   Getting chemical shift information

Click the Zoom icon and zoom in to the downfield region of the spectrum at approximately 8.3-7.1 ppm.

Select the Measure/Cursor Position command (or you can click the Cursor Value icon in the toolbar). The cursor becomes a vertical half-crosshair. Move the cursor over the spectrum. Information on the chemical shift and peak height appears on the status bar. To exit, press <Esc>.

22.   Getting J-coupling information

Select the Measure/Distance/Separation command. Click the tops of two neighboring peaks, such as the set at 7.71 and 7.69 ppm. The separation value, ~ 7 Hz in this example, appears on the status bar.

To exit, press <Esc>.

23.   Identifying peaks

Select the Preference/Pick Parameters command. Click the Cursor button. When the cursor becomes a large horizontal line, position it to give a threshold below the lowest peak and click the mouse button. In the control panel, acknowledge the threshold by clicking OK.

The threshold is the "lowest" intensity defined as a peak and is used to avoid selecting noise as peaks.

Select the Peaks/Pick All command. Click OK.

This labels all peaks, and displays a peak table.

Now select the Peaks/Remove Region command. Again drag to select a region.

FELIX removes the labels from the deselected peaks.

Select the Peaks/Pick One command (or right-click the spectrum and then select the Pick One Peak item from the context menu); click the tops of a few of the deselected peaks; then press <Esc> to display the values.

Select the Peaks/Remove All command. Click Delete.

24.   Annotating the spectrum

Select the Edit/Annotation command (or click the Annotate icon from the toolbar). Enter a name ann for the annotation file in the resulting control panel and click OK.

FELIX displays a modeless ANNOTATIONS dialog.

Click the Roman Text button. Move the large crosshair to the desired starting point for text inside the frame and click the mouse button. Type your text (such as peak 1) in the Text box and click OK.

Click the Arrow button. Move the crosshair underneath the text, and drag it towards the top of a peak.

Click the Parameters button.

Notice that many options can be adjusted in the new control panel.

Click Cancel to exit the control panel, then click Done to leave the Annotations control panel.

25.   Exiting FELIX

To exit FELIX, select the File/Exit command.