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Define Peaks

Define Peaks

NUTS Help

DP — Define Peaks

This subroutine allows manual peak picking using the cursor, and allows the user to place labels on the peaks. (Note that DP is not included in NUTS Lite.)  A summary of the DP subcommands is given at the bottom of this section. Show me how to use DP.

The DP routine operates similarly on both 1D and 2D files. For 1D files, DP is an alternative to the automatic peak picking (PP) command for creating a list of only selected peaks. Once peaks have been selected in DP, a chemical shift or other label can be placed above the peak by typing Ctrl-P. On entering the DP routine, the cursor changes to a small crosshair labeled DP and the menu selections change. Commands are single-letter commands which are executed immediately. With the exception of functions which require the mouse, all commands can be accessed via the menus.

Position of peak labels — By default, peak labels for 1D spectra are displayed at the top of the screen, with short lines drawn to show which peak corresponds to each label. The labels can alternatively be displayed just above the top of each peak. This can be set for all peaks in the nuts.ini file, or for each peak from within the DP routine by bringing up the parameters of a selected peak (see edit, below). NUTS now has some "smarts" to attempt to avoid overlap of labels on adjacent peaks. Labels can also be moved using the mouse (see moving labels, below).

Selecting peaks — When the DP routine is entered, peaks can be selected by clicking the left mouse button. For 1D spectra, a vertical red line is drawn showing the point that was selected. For a contour or intensity map of a 2D file, a small cross is placed on the peak. Once selected, the peak labels can be displayed by typing Ctrl-P. By default, NUTS chooses the nearest maximum point (positive or negative) which it can find. This "Snap to" feature can be turned off from the Edit menu to allow picking shoulders, etc.

Automatic peak picking — Automatic peak picking of 1D spectra is also available within DP from the Edit menu or by typing A. This uses the minimum height (MH) and RMS noise factor (RM), in the same way as PP.  Automatic peak picking of 2D spectra is only available with the new Arrayed Mode option, which allows the entire data set to be placed into memory.  A set of peaks from one 2D spectrum can be overlaid on the display of a different spectrum.  See 2D compare.

Deleting peaks — Any peak can be deleted by placing the cursor on or near the peak to be deleted and typing K (Kill). (Note: Do NOT click the mouse button to do this, just position the cursor.) The K command will always delete a peak, whichever one is closest to the cursor at the time K is typed. All peaks can be deleted by typing C or choosing Clear Selected Peaks from the Edit menu.

Labels in Hz or ppm — To display the peak position in Hz instead of ppm, type H. To display the text label instead of the chemical shift, type I. By default, the text label is the number of the peak, in the order selected. This is to allow correlation between peak labels and a peak list generated by PP. Both commands are also available from the Edit menu. Selected labels can be displayed as text even if all others are labeled with Hz or ppm. This is done by displaying the parameter dialog box for the selected peak (see edit, below) and checking the box labeled "Show Info label only". Note that this causes the text label even when other peak labels are toggled off with Ctrl-P or PF. This can be used to put multiple text labels on the screen, which need not be associated with a specific peak.

Creating a peak list — The peaks selected are entered into a list containing shift, peak intensity and a peak label (eg., descriptive text) in the order the peaks were selected. The list can be reordered from largest to smallest chemical shift by selecting Reorder from the Edit menu or by typing # (number sign; shift-3 key). The list can be placed into the Windows clipboard for pasting into another document such as the Notepad by selecting Type List to Clipboard from the Edit menu or by typing T. If peaks are added, deleted or reordered, be sure to execute the T command again to update the clipboard contents before pasting the list into another document. If the clipboard display feature is enabled (by typing C or Ctrl-B or from the Edit menu), the T command displays the list on the screen. Repeat the T command as peaks are added, deleted or reordered to see the current list.

The columns in the list can be separated by spaces or by tabs, according to the setting of the TB (Tabs) parameter. 

A peak list containing only ppm values and peak label can be copied to the clipboard using subcommand P.  The columns are separated by tabs.

Editing peak labels — The information about each peak can be viewed by placing the cursor on or near the peak of interest and clicking the right mouse button. The dialog box shown below is displayed which shows the peak frequency, relative intensity, etc.

The bottom line is a label that can be edited for each peak. By default, the peak number is placed in the label box, but this can be edited to be any other text label. There is a check box which allows the user to choose to display the peak labels either horizontally or vertically for each peak independently. This preference can also be set in the nuts.ini file. There is a check box labeled "Show first argument only". This is for situations where extensive information has been input in the text label box, which can be too long to display above each peak. If this box is checked, only the characters up to the first space are used to label the peak. This could be the case if the user enters extensive comments such as substructure codes and assignments to be saved in the file’s tailer.

This dialog box is the same whether the current spectrum is a 1D spectrum or a 2D contour map. (Slices from a 2D data set are treated the same as 1D spectra.) The box labeled "Relative Area" is used for volume integrals of 2D peaks. Enter a value for a chosen peak and the volume of all other peaks will be scale appropriately. See the description of volume integrals for details.

Font — The font used for peak labels can be changed by typing FV or FH (for vertical and horizontal fonts, respectively) or selecting Set Fonts from the Edit menu.

Moving peak labels — Beginning with version 5.09, it is now possible to adjust the position of each peak label using the mouse. Position the cursor on the label of interest, press and hold the left mouse button and drag the label to the desired position. The position of any peak label can also be changed in small steps up, down, right and left. To do this, place the cursor near the peak whose label will be moved and type U (up), D (down), L (left) or R (right). Do not click the mouse button to do this, just position the cursor. A label can be moved multiple steps in each direction. Note that the labels may look slightly different o
n the screen and on plots.

The list is not lost when the DP routine is exited, so it is possible to exit DP, choose a different region and re-enter DP to add more peaks to the list. Note that, for this reason, it is a good idea to delete all peaks (with C) on entering DP to operate on a new spectrum, so that peaks selected in the previous spectrum aren’t carried over.

Saving peaks with the spectrum — The list of selected peaks is saved with the file, and can be recalled at a later time with the TA command. The list of peaks can also be saved to a text file by choosing Save to File from the File menu or typing S. A peak list can be loaded from a previously saved file by choosing Get File from the File menu or by typing G. This command retrieves a set of chemical shifts from the file and applies those peak positions to the current spectrum, drawing red lines on the screen to indicate selected peaks.

Subcommands:

A — Automatically pick peaks (Minimum Height must be set before entering DP)
C — Display contents of clipboard on screen (same as Ctrl-B command)
G — Get peak file. Recalls previously saved peak list and displays the corresponding peaks, deleting any peaks which had been selected.
H — Label peaks with Hz, rather than PPM
I — Label peaks with text label, rather than chemical shift.
K — Delete the selected peak closest to the cursor location
P – Copy ppm list to the clipboard
S — Save peak file.
s — Save peak file in format consistent with SpecMan (from Spectrum Research)
T — Copy peak list to the clipboard
Z — Zero out all selected peaks.
# — Re-order the peak list, from highest to lowest chemical shift
Ctrl-C — Copy screen to Windows clipboard as bitmap See copying spectra.
Alt-C — Copy screen to Windows clipboard as Metafile

The need for the following 4 commands has been removed, now that peak labels can be moved with the mouse. However, at this time the commands still work. Each command operates on the selected peak closest to the cursor.

D — Move peak label Down a small amount
L — Move peak label Left a small amount
R — Move peak label Right a small amount
U — Move peak label Up a small amount

Volume Integrals of 2D peaks

The Define Peaks subroutine is used to select peaks whose information is entered into a list. This information includes chemical shift in both dimensions, an editable peak label and relative peak volumes.

Begin by entering DP and select peaks of interest by clicking with the left mouse button. Choose one peak whose volume is to be assigned and click with the right mouse button on or near that peak. Enter a value for volume in the box labeled Relative Area. Areas (volumes) of other peaks will be scaled to this value.

The Arrayed Mode allows automatic peak picking, including volume integrals.

Several points must be kept in mind when using this feature. The limits used for integration are determined by the minimum height (MH) command. The integral is the sum of all points in the vicinity of the peak whose intensity is greater than the minimum height value. This is done by starting at the peak maximum and "walking" in each direction, summing each point until the minimum height is reached. This summation is performed at the time the peak is selected, and is the value shown for Absolute Area. Setting the value of a chosen peak merely enters a scaling factor to give "nicer" numbers for the peak volumes. If a new value for MH is entered, the list of selected peaks must by cleared (by typing Z) and peaks reselected. Care must also be taken that a chosen peak is resolved from neighboring peaks at the level of the minimum height.

Control-P — Toggle peak labels on/off

Peaks which have been selected in the Define Peaks subroutine can be labeled with their chemical shift or a text label by typing Control-P. This is a toggle, so typing it again removes the labels. In Links or macros, use " ^P ".

PN — Turn peak labels on

Peaks which have previously been selected in the Define Peaks subroutine can be labeled on the screen and plots by typing PN. Display of the labels can be turned off by PF. These commands perform the same function as Ctrl-P, which acts as a toggle.

PF — Toggle peak labels off

Peaks which have previously been selected in the Define Peaks subroutine can be labeled on the screen and plots by typing PN. Display of the labels can be turned off by PF. These commands perform the same function as Ctrl-P, which acts as a toggle.

Automatic 2D Peak Picking (Arrayed Mode only)

Automatic peak picking of 2D data is now available in the Arrayed Mode.  While in Arrayed Mode, with an intensity plot displayed, enter the DP routine and type A to perform automatic peak picking, shown below, including automatic volume integration.

List generated by automatic peak picking:

LINE     POINT   SLICE     PPM1        PPM2    INTENSITY    AREA   LABEL   1         36      15     79.876      3.401     96.783      0.77   1   2        101      29     68.982      3.074     79.186      1.22   2   3        131      13     64.077      3.439     60.209      1.02   3   4        146      21     61.703      3.254     79.742      0.97   4   5        155      35     60.209      2.920     55.281      1.21   5   6        156      32     60.043      2.997    112.151      2.15   6   7        164      46     58.733      2.666     79.937      0.82   7   8        175      51     56.891      2.538     92.602      1.50   8   9        217      33     49.866      2.977     79.109      1.17   9  10        223      40     48.950      2.811     78.639      1.00   10  11        230      33     47.787      2.982     84.700      1.26   11

 

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Last updated: 3/6/06.