Peak

The Peak menu provides direct access from selected peaks in a spectrum window to the Analysis functions related to peaks.

Selected peaks...

Displays a table of the currently selected peaks using the popup Peaks: Selected Peaks. Selected peaks are shown as boxed within the spectrum windows. The peaks in the table may be assigned, unaliased, moved and edited generally. Peaks can be directly searched for and marked or stripped in the spectra.

Add new peak

Creates a new peak at the current cursor position. Note that a peak will be created in all of the currently displayed spectra in the window.

Center z planes on peak

This command moves the view of the spectrum in the orthogonal dimensions (z1, z2 etc.) such that it coincides with the centre of the current peak.

Delete selected peaks

Deletes all of the currently selected peaks after confirmation by the user.

Find close peaks

Finds peaks that are close in chemical shift for a specified peak dimension. Find close peaks options are dependent on the chemical shifts of the peak, and the spectra defined in the project. For example:

• • F1: 1H 8.234 ppm

    • 15N-HSQC:15N-HSQC.spc

    • CBCAcoNH:CBCAcoNH.spc

  • F2: 1H 3.423 ppm

    • 15N-HSQC:15N-HSQC.spc

    • CBCAcoNH:CBCAcoNH.spc

  • F3: 15N 110.337 ppm

    • 15N-HSQC:15N-HSQC.spc

    • CBCAcoNH:CBCAcoNH.spc

The resulting close peaks are listed in Peaks: Selected Peaks and are ranked according to chemical shift difference.

Find symmetry related

Finds peaks that are related by symmetry. 

Use strips

Display the results as strips in a spectrum window.

Use tables

Display the results in the Peaks: Selected Peaks popup.

Label Auto Arrange

Arranges the labels of the selected peaks automatically to minimise overlap of peak labels. A convenient tool to optimise the spectrum view.   

Label Position Reset

Resets the positions of the labels of selected peaks to their default value. Reverses the action of the command Label Auto Arrange.

Make intermediate peak

Creates a new peak at the mean position of the selected peaks. New peaks are created only from peaks in the same peak lists.

Match peaks

This option finds peaks in spectra with similar dimension that match the position(s) of the selected peak(s) in a given dimension.

For example, by selecting a peak in a 3D 15N-NOESY-HSQC experiment, peaks with similar indirect (F2) proton chemical shifts can be found in a 3D 15N-TOCSY-HSQC experiment with this option. The matched peaks can have different direct proton and heavy atom shifts. Match peaks options (the target spectra and dimension) are dependent on the spectra that are defined in the project. For example:

• • In 15N-NOESY:15N-NOESY-HSQC.spc:2

    • F1

    • F2

    • F3

  • In 15N-TOCSY:15N-TOCSY-HSQC.spc:3

    • F1

    • F2

    • F3

  • In active spectra

    • F1

    • F2

    • F3

Match peaks opens Peak Groups to view the matched groups of peaks and display them in window strip regions.

Set details

This command allows the user to add a comment to the peak using the Peak Details popup.

Set merit

Sets the merit value of a peak. Merit values are indicators for the quality of the peak and can be used to change a peaks annotation in Peaks: Draw Parameters and merit thresholds may be set for some analyses, e.g. calculation of distance constraints. Merit values are:

• • 0.0

  • 0.5

  • 1.0

Show structure connections

Opens Structure: Structure Viewer to display the atoms to which the currently selected peaks are assigned. Only works if an appropriate structure is present in the project. Any peak with two assigned hydrogen dimensions will have a connection drawn between the hydrogen atoms or atom sets - e.g. methyls.

Snap selected peaks

Moves selected peaks to the nearest maximum. Useful to, for example, move copied or imported peaks to their maxima in a new spectrum that was not originally used to pick the peaks.

Strip plot selected peaks

Creates strip plots at peak positions in the window for the selected peaks. The strip y positions will be the average y position for the selected peaks. Maximum number of strips is 15.

Unalias peak

Opens the Edit Peak Aliasing popup, which allows the user to specify how may times the peak position has been aliased in each dimension. Specifying the correct number of aliasing allows the calculation of the appropriate unaliased peak position.

Unaliasing propagate

This option sets the aliasing for all of the currently selected peaks to be the same as the peak under the mouse cursor.

Unite resonance positions

Unites the resonance and peak positions of the selected peaks to be the same as the peak under the mouse cursor.

Zoom to selected peaks

Makes the spectrum window zoom in and center on the selected peaks.

Zoom to spin system peaks

...

Re-reference to this peak

Used to re-reference a spectrum (moving) based on another spectrum (fixed). The re-referencing requires the selection of 2 peaks, one in the fixed spectrum and one in the moving spectrum. The peak in the fixed spectrum should be kept under the mouse cursor. Re-reference to this peak opens the Reference By Peak popup.