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.
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.
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. |
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.
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.
FELIX calculates a value for the baseline from the last 20% of the data points and subtracts that value from each data point.
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).
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.
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.
This removes the real-time phase interface and makes the phased spectrum appear in the graphics frame.
6. Performing the baseline correction
After FELIX selects the baseline points, it marks their locations with red tics at the bottom of the display frame.
FELIX applies the polynomial function to the spectrum.
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.
FELIX calculates the integral of the peaks and displays the integral on the spectrum.
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.
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.
If not done yet, set up the tutorial files as described in "Setting up tutorial files" on page viii.
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.
Now you proceed to manipulate files and workspaces.
Select the File/Open command. Set the following parameter values in the dialog box:
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.
FELIX close the original window and displays four small windows, the last one being the active one.
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.
FELIX displays a fifth frame. All frames are automatically arranged.
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:
Now select the Process1D/Zero Fill command and set these values:
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.
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.
The FID is now multiplied with the window function and you see the results.
The Fourier transform produces the NMR spectrum.
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.
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.
13. Baseline-correcting the spectrum to eliminate the curved baseline
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.
FELIX displays a new window with a spreadsheet. You may scroll through the selected baseline points.
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.
17. Using real-time sliders to compare two different spectra
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.
18. Getting the difference between two spectra
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
20. Setting the reference on water peak
FELIX redisplays the spectrum with new ppm units.
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
The threshold is the "lowest" intensity defined as a peak and is used to avoid selecting noise as peaks.
This labels all peaks, and displays a peak table.
FELIX removes the labels from the deselected peaks.
FELIX displays a modeless ANNOTATIONS dialog.
Notice that many options can be adjusted in the new control panel.