IU NMR user guide

Basic VNMR Commands/macros for Peak Picking

• dpf ...... display peak frequencies over spectrum,
• ppf ...... plot peak frequencies over spectrum,
• dll  ...... display a peak list with frequencies and intensities,
• pll  ...... plot a peak list with frequencies and intensities,

while a parameter th controls threshold for peak picking. The frequency unit is specified by axis. An additional macro ppfhz will plot peak frequencies in Hz with regardless of axis.

A noise-factor argument could be used with dpf, ppf, ppfhz, and dll to specify the noise factor for peak picking, e.g., dpf(1.5). The default is 3. A smaller value results in more peaks to be picked. dpf(0) will pick all peaks above th.

More Enhanced by IUNMR Staff

Peak picking with suppression of large peaks

1. Set peak picking cutoff:
• adjust the position of the th horizontal line so that the large peaks which you don't want to pick are above the line while those to-be-picked peaks are below the line,
• type llcut  ...... set the current th value to the cutoff parameter th0
2. Set peak picking threshold:
• adjust the position of the th horizontal line (you may need to click on the th button in the 1D display menu to toggle the th line display ON) to set the peak picking threshold as usual,
3. Peak picking:
• the IUNMR macros sdpf, sppf, sdll, and spll can be used, in the same manner as dpf, ppf, dll, and pll, respectively, to pick the peaks whose height is greater than th but less than th0.

User manually marked frequencies

A VNMR command (or button) mark can be used for user to mark peaks or frequencies by hand. These user-marked frequencies (and their intensities) could then be displayed or plotted using the IUNMR macros mdpf, mppf, mdll, and mpll. General procedures are:

1. type mark('reset')   ...... clear the user-marked frequency list
2. click on a peak
3. type nl   ....... let the computer move the cursor at the nearest peak
4. type mark  ...... add the peak to the list
5. click on next peak
6. type nl mark  …... mark the next peak, and so on and so on
7. type any of the following macros as desired
• mdpf ...... display the user-marked peak frequencies over spectrum
• mppf ...... plot the user-marked peak frequencies over spectrum
• mdll  ...... display the user-marked peak list with frequencies and intensities
• mpll  ...... plot the user-marked peak list with frequencies and intensities

Add user-marked peaks to the (computer) peak picking list

The above user-marked peaks can be added to the computer peak picking list (as generated by dpf, ppf, dll, and pll). This feature is very useful when you want to add a few peaks which were not picked by computer peak picking (dpf/ppf/dll/pll) to the peak list. The following IUNMR macros could be used to do so:

• amdpf ...... display computer picked and the user-marked peak frequencies over spectrum
• amppf ...... plot the computer picked and user-marked peak frequencies over spectrum
• amdll  ...... display computer picked and the user-marked peak list with frequencies and intensities
• ampll  ...... plot computer picked and the user-marked peak list with frequencies and intensities

The parameters and arguments (threshold, noise-factor, etc.) which are used for dpf/ppf/dll/pll can be used for amdpf/amppf/amdll/ampll in the same manner.

If you do not want large peaks (such as solvent peaks) in the spectrum to be picked by amdpf/amppf/amdll/ampll, the "S" version of these macros, samdpf, samppf, samdll, and sampll are also available (see "Peak picking with suppression of large peaks" section about how to set cutoff). Please note that only computer picked peaks are limited by cutoff (th0), not user-marked peaks. Therefore, it is possible to suppress numerous large peaks from the peak list (which is generated by computer peak picking) but remain few large peaks which were manually marked.