In Lesson 1: Introduction to 1D processing, you learn the basics of loading and processing 1D data files.
The topics covered in this lesson are:
In Lesson 2: Advanced 1D processing, you learn some of the many options available for processing 1D data.
The topics covered in this lesson are:
This lesson is designed to introduce the FELIX novice to some of the commands required to process a one-dimensional data set.
In this tutorial session you will process a 1D NMR data set that is supplied with this distribution.
The following files from the $BIOSYM/tutorial/felix/1D_tut/1 directory are required for this lesson. Please copy these files to your working directory:
Move to your working directory (if it's not your current directory) and enter felix at the system prompt to start the program.
Select the File/Open command. Set the File Type parameter to Other Data, and then select the fid file from the Files value-aid by clicking its name in the list. Select OK to confirm the selection.
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.
Select the Process1D/DC Offset command and toggle the Type on to obtain Oversample DBC. Select 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.
Select the Process1D/Window Function menu item to obtain a control panel that prompts for a window function. Enter Exponential as the Window function and select OK. In the following control panel, enter 0.2 for Line Broadening and select OK to multiply the data by an exponential window function.
The display is updated to show the results.
5. Fourier-transforming the data
Now you 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 menu item. FELIX automatically determines that the transform type should be Oversampled FFT. Select OK.
The result is a spectrum in the graphics frame. Notice that the spectrum requires some phase correction, which is most easily applied first using the phase parameter values from the procs file.
Select the Process1D/Phase Correction menu item. Set the Method to Parameter and leave the Zero and First Order parameters at their current values (136.912 and 14.55447, respectively). Select 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 menu item and select the Realtime option. Use the sliders to adjust the pivot point position, the zero-order phase correction (Phase0), and the first-order phase correction (Phase1).
Do this by putting the cursor over the slider that corresponds to the desired function, then moving the slider by clicking and holding the mouse button while moving the mouse. When the desired effect is achieved, release the mouse button.
Repeat this with each correction until you are satisfied with the spectrum, then click the Keep button to exit the interface.
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 menu item. Toggle the Baseline Point to on and leave the parameter at Auto Pick Points alone. Select OK. In the next control panel, leave the Interval size at 128 and Maximum Deviation at 5 and select OK.
After FELIX selects the baseline points, it marks their locations with red tics at the bottom of the display frame.
Again select the Process1D/Baseline Correction menu item, but now toggle the Baseline Correction to on and select the Polynomial option. When the control panel appears that prompts for the Polynomial order, select OK to select the default of 5 (fifth-order polynomial).
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.
To exit FELIX, select File/Exit to begin the shutdown sequence. You must turn off the Save Current Session and Save Current Database parameters and then select OK.
This shuts down FELIX without saving the baseline points or integrals in the database file that 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.
The following files from the $BIOSYM/tutorial/felix directory are required for this lesson. Please copy these files to your working directory:
Move to your working directory (if it's not your current directory) and enter felix at the system prompt to start the program.
The database is a binary file where FELIX stores data like segments, baseline points, 2D peaks, volumes, etc. The Edit/Table menu item gives you access to all data stored in the database. The File/Export/ Table and File/Import/Table menu items allow you to read and write the data as ASCII files.
Now you proceed to manipulate files and workspaces.
Select the File/Open menu item. 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. If non- Bruker data are desired, select a different file.
The original window is divided into four frames.
The FID is plotted in frame 4.
Activate a second frame by clicking its header. Select the File/Open menu item. Enter sample2.dat as the Filename and select OK.
A different FID is shown in the new frame.
A fifth frame is formed on top of the earlier four frames.
To close Frame 5, double-click the frame close widget (the small rectangle in the upper-left corner of Frame 5).
6. Returning to a single frame and reading the FID
Select the Preference/Frame Layout menu item and choose the Default option. This returns the screen to a single frame. If the FID is not in the frame, read it in as in Step 3.
Note the minimize, close, and maximize buttons in the frame header.
7. Processing the data to create a spectrum
Select the Process1D/DC Offset menu item. Set the following parameter values in the control panel that appears:
Now select the Process1D/Zero Fill menu item 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.
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!
Select the Process1D/Window Function menu item. In the control panel, choose Exponential and select OK.
A new real-time widget appear on the screen. You are now in the interactive viewer mode.
The mathematical function is drawn over the FID in red.
Using the slider you may change the parameters for the displayed window function and the effect on the FID.
Click Keep. The FID is now multiplied with the window function and you see the results. The window function and its parameters are printed in the text frame.
The Fourier transform produces the NMR spectrum.
Data collected from some Bruker instruments is stored differently than data from other instruments, and hence a special transform is needed. This is important. If you do not want to use Bruker data and want to use a different transform, use one of the other 1D data sets provided in the $BIOSYM/tutorial/felix directory.
Note also that 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 have to use the normal ft command in FELIX.
This is an interactive phasing mode. A set of sliders and buttons appears. The data may be expanded vertically by using the keypad functions.
Set the pivot for the spectrum by <Shift>-clicking the right mouse button under the spectrum at the position where you want the pivot point to be. Now drag the Phase0 and Phase1 sliders to the far right.
The values of the phasing parameters are displayed to the right of the sliders.
11. Phasing an expanded region
Click the Expand button. When the cursor becomes a +, position it to one side of the region to be expanded (for example, to the left of the left-most peak). Press the mouse button and drag the cursor to the other side of the region (for example, the right side of the left-most set of peaks). Release the button, and the selected region fills the window. Continue adjusting the Phase0 and Phase1 sliders to phase the spectrum.
Click the Full button to view the entire spectrum. When satisfied with the phasing, click the Keep button.
12. Baseline-correcting the spectrum to eliminate the curved baseline
Select the Process1D/Baseline Correction menu item. Toggle the Baseline Point to on and choose the Auto Pick Points option. Select OK.
This generates a set of baseline points displayed as small red lines under the spectrum to be used in the correction.
13. Adding user-defined base points
Select the Process1D/Baseline Correction menu item. In the control panel that appears, toggle the Baseline Points to on and select the Pick Points Via Cursor option. When the cursor becomes a large +, move the vertical bar of the 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. Continue until you have defined all the desired baseline points. To quit the +, click in the black blank area or press the <Esc> key.
A spreadsheet editor appears and you may scroll through the selected baseline points.
15. Applying the baseline correction
Select the Process1D/Baseline Correction menu item. In its control panel, select either the Polynomial, Cubic Spline, or Real-Time Polynomial option. Select OK to apply the correction to the selected basepoints.
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. Depending on the order of polynomial, the display looks different. You can change the polynomial parameters, up to the order of nine.
16. Using realtime sliders to compare two different spectra
This pushes the spectrum you have been working with to the top of the screen.
Read the 1D file sample.dat into the workspace as in Step 3. Apply zero filling and a different window function, e.g., Sinebell^2, using 16384 and 90.0 for parameters. Transform the FID and use the Process1D/Phase Correction menu item with the Parameter option to apply the phase correction.
The parameters for the phasing are stored internally. After the real-time phasing, you can use the same parameters automatically when using the Parameter option in the Phase Correction command.
Set the parameters so that the spectra are plotted in different colors. Select the Preference/Plot Parameters menu item and set Color Scheme to Define, Number to 1, and Cycle to 2. Select OK.
Select the Preference/1D Scale menu item. Use the mouse to change the overlap to 1, to put the red spectrum on top of the white one.The difference between the two should be noticeable.
The sliders are controlled by FELIX commands that you can use in your own macros (see the Real-Time Displays chapter at $BIOSYM/doc/ felix/05_RealTimeDisplays.html).
By selecting the Tools/Buffers/Pop Work from Stack Top menu item, you restore the original view. The second spectrum is deleted.
17. Viewing an expanded region
Select the View/Limits/Manual Limits menu item. The control panel that appears shows the current upper and lower values of the displayed region. If you want a different region, enter different values:
Set the following parameter values (within Points) to select the region around the water resonance:
The display is updated to include only data in the 7000-9000 point region.
In this example you have to do the selection in points. If you have referenced your spectrum and/or changed the display units to ppm you have to choose the region in ppms.
The current limits information can be written to a file using the File/ Export/Plot Limits menu item. The information can then be recalled later, for example, when comparing other spectra.
18. Setting the reference on water
Select the Preference/Reference menu item. Select the Cursor button, and the cursor becomes a vertical line. Now click the water resonance (at ~8200 points). A control panel appears. From the Axis Type popup select the Ppm option. Set Reference PPM to 4.76 and select OK.
19. Returning to the full spectrum
The axis is now in ppm, with the water resonance near the center of the spectrum, at 4.76 ppm.
20. Viewing and examining a region of resonances
Now select the View/Limits/Set Limits menu item. The cursor becomes a cross. Drag to select the downfield (left-most) set of peaks, at approximately 8.3-7.1 ppm.
The selected region fills the frame.
21. Getting chemical shift information
Select the Measure/Cursor Position menu item. The cursor becomes a vertical half-crosshair. Move the cursor over the spectrum. Information on the chemical shift and peak height appears in the text frame. To exit, press <Esc>.
22. Getting J-coupling information
Select the Measure/Distance/Separation menu item. 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 in the text frame.
To exit, click in the blank space next to the spectrum or press <Esc>.
Select the Preference/Pick Parameters menu item. Set the Threshold Value to Cursor and select OK. 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 repeatedly displayed control panel, acknowledge the threshold by selecting OK.
The threshold is the "lowest" intensity defined as a peak and is used to avoid selecting noise as peaks.
The labels are removed from the deselected peaks.
Select the Peaks/Pick One menu item, click the tops of a few of the deselected peaks, then click a blank spot to display the values.
Select the Edit/Annotation menu item. Make sure a filename is entered in the resulting control panel and click the Build button.
Select the Roman Text menu item. 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 select OK.
Select the Arrow command. Move the crosshair underneath the text, and drag it towards the top of a peak.
Notice that many options can be adjusted.