Processing 2D Experiments

See also Acquiring a 2D experiment

Processing a 2D Absolute-Value experiment:

1. Click on main menu, process, select params, pseudo, and large. If this spectrum will be symmeterized or if the spectrum will be automatically analyzed with the acosy program, set fn1=fn.
2. Optional (and recommended): Click on main menu, process, adj weighting to adjust the weighting applied to the FID data.
3. Optional: To apply a drift correction to the data, type wft2d('t2dc','t1dc'). To apply a first-order baseline correction to the data, type wft(1). If no peaks are present, type wft(20) or wft(100). Type dc cz intmod='partial' region to define baseline points. Define more baseline points as needed by positioning the cursor at the new point in the spectrum and typing z. Type wft1d bc('f2',1) wft2d bc('f1',1). To apply a higher-order baseline fit, type wft1d bc('f2',<order number>) wft2d bc('f1',<order number>).
4. Type wft2d to weight and fourier transform the data in both dimensions.
5. A 2D spectrum may be symmetrized to remove vertical and horizontal streaks and noise. However, symmetrizaion can generate peaks that appear to be cross peaks. ALWAYS compare a symmeterized spectrum with the unsymmeterized spectrum before making final conclusions. Spectra with fn=fn1 and sw=sw1 may be symmeterized. Type foldt to symmeterize the spectrum.
6. Type acosy to automatically analyze a COSY data set with fn=fn1 and sw=sw1.

Processing a 2D Phase-Sensitive experiment:

1. Click on main menu, process, select params, pseudo, and large. Click on >PH to choose phase sensitive processing. If this spectrum will be symmeterized or if the spectrum will be automatically analyzed with the acosy program, set fn1=fn.
2. Optional: Click on main menu, process, adj weighting to adjust the weighting applied to the FID data.
3. Optional: To apply a drift correction to the data, type wft2da('t2dc','t1dc'). To apply a baseline correction to the data, type wft(1). If no peaks are present, type wft(20) or wft(100). Type dc cz intmod='partial' region to define baseline points. Define more baseline points as needed by positioning the cursor at the new point in the spectrum and typing z. Type wft1d bc('f2',1) wft2d bc('f1',1). To apply a higher-order baseline fit, type wft1d bc('f2',<order number>) wft2d bc('f1',<order number>).
4. Type wft2da to weight and fourier transform the data in both dimensions.
5. A 2D spectrum may be symmetrized to remove vertical and horizontal streaks and noise. However, symmetrizaion can generate peaks that appear to be cross peaks. ALWAYS compare a symmeterized spectrum with the unsymmeterized spectrum before making final conclusions. Spectra with fn=fn1 and sw=sw1 may be symmeterized. Type foldt to symmeterize the spectrum.
6. Type acosy to automatically analyze a COSY data set with fn=fn1 and sw=sw1.

Displaying the 2D Spectrum:

1. When the 2D experiment is processed, a spectrum is displayed which usually shows the "floor" of the spectrum (vs too high and th too low). Type nm2d to automatically adjust the parameters vs and th to produce a reasonably scaled 2D spectrum. Adjust th to change the lowest threshold level of the contour plot (type th=<new number>) or click on the "th" color bar to the right of the spectrum (color map mode only). Adjust vs to change the vertical scale of the spectral peaks (type vs=<new number>), or move the mouse arrow to a noise peak and press the center mouse button, or move the mouse arrow to a position where a peak should appear and press the center mouse button.
2. Click on main menu, display, size, and select full, or select full with traces if you want to display traces or projections.
3. Click on main menu, display, contour to switch from color map mode to contour mode. Type dconi to redraw the color map and manipulate the 2D spectrum.
4. To expand a region of the 2D spectrum, click on main menu, display, contour, and box. Then move the bottom/left cursors with the left mouse button, and move the right/top cursors with the right mouse button. Click on main menu, display, contour, expand to expand the region.
5. To reference the 2D spectrum, position the cursor over a peak and type rl(<ref number>hz) and rl1(<ref number>hz). [As of 6/1/94, the non-acquisition dimension of a heteronuclear experiment is incorrectly referenced by this procedure.]
6. Click on main menu, display, contour, and traces to show the 1D spectrum at the position of the horizontal cursor in the 2D spectrum. Move the horizontal cursor by clicking or dragging the cursor with the left mouse button. Position the mouse arrow over the 1D trace above the 2D spectrum and click the center mouse button to adust the 1D trace vertical scale.
7. Click on main menu, display, contour, Proj, and Hproj(max) to show the horizontal 1D projection of the 2D spectrum. Position the mouse arrow over the horizontal projection and click the center mouse button to adust the vertical scale. See also step 25 about plotting projections. Click on Plot to plot the projection (plotted when you type or click on page). Repeat this step and click on Vproj(max) to display the vertical projection.
8. Type grid to show a grid over the spectrum.
9. Type ds2d to display a stacked plot.
   

Plotting the 2D spectrum:

1. Click on main menu, more, config, select plotter to select HP7550A (HP pen plotter) or LaserJet_300R (HP Laser Jet).
2. To plot projections of the 2D plot, see step 21. To substitute the 1D reference spectrum of step 3 for the horizontal projection of a homonuclear 2D experiment, join a different experiment, process the 1D reference spectrum and then type sc=6 wc=180 vp=120, and adjust the vertical scale of the spectrum with the middle mouse button. Then type pl and then return to the 2D experiment. For HP7550A, type sc=10 wc=288 vp=132 and for Laser Jet type, sc=10 wc=180.
3. Click on main menu, display, plot and select all contours for spectra with positive and negative peaks or pos. only for spectra with only positive peaks. Click on params to plot acquisition parameters.
4. Type pacosy to plot the automatic analysis of the COSY experiment.
5. Type page to generate the plot.