This popup allows the user to pick 3D peaks based on a 2D root peak list from a 15N-HSQC, and it allows to propagate assignments from the 2D peak list to the 3D peaks. The advantage of this method for picking peaks in higher dimensional spectra is that the search for peaks is limited to the regions where peaks are expected, which prevents noise peaks from being picked. In addition, the functionality guides the user through the regions where the 3D peaks are expected (and picked), which provides a convenient way to perform the necessary manual inspection of the peak picking and assignment. The user first specifies the options in the {Navigation Windows} and {Spectra & Tolerances} tabs, and then proceeds to the actual peak picking using the {Link Peaks} tab.

Navigation Windows

The {Navigation Windows} tab allows the user to select the windows in which the navigation in the higher dimensional spectra will take place. The navigation windows that can be selected depend on the root peak list that is used as a basis for the peak picking.

The Assignment: Link Peak Lists popup (Navigation Windows).

Root Peak List

Specifies the peak list that is used as a basis for the picking of the higher dimensional spectra.

Root Window

Specifies the window in which the spectra and peaks of the root peak list are displayed.

Navigation Windows table

The table containing the list of navigation windows.

#

The number of the navigation window.

Name

The name of the navigation window.

Selected Mapping

Specifies the selected mapping that is used in the navigation window.

Remove Window

Removes the selected navigation from the list of navigation windows. This does not affect the window itself.

Add Window

Adds the window that is selected in the windowPulldown to the list of navigation windows, if that window is not present in the list yet.

windowPulldown

This pulldown allows the user to select a window to the list of navigation windows. The pulldown options depend on the Root Peak List and the dimensions it contains: In case of a 15N-HSQC root peak list, only those windows will be listed that have 15N and 1H axes.

Spectra & Tolerances

The {Spectra & Tolerances} tab allows the user to select the spectra for which peaks will be picked, and various options such as tolerances for the peak picking.

Important note: Spectra are only included in the Assignable Spectra list if they are visible in the spectrum windows. In case a spectrum is missing from the list, check if it is visible in the navigation window.

The Assignment: Link Peak Lists popup (Spectra & Tolerances).

Root 1H Dim 1

Specifies the tolerance in the 1H dimension of the root peak list that is used for the higher peak search in the assignable spectra.

Min Water

Specifies the minimum chemical shift for the water line. Regions between the minimum and maximum chemical shift for the water line will be excluded from the peak picking.

Max Num Marks

Sets the maximum number of marks to be displayed in the navigation windows.

Root 15N Dim 2

Specifies the tolerance in the 15N dimension of the root peak list that is used for the higher peak search in the assignable spectra.

Max Water

Specifies the maximum chemical shift for the water line. Regions between the minimum and maximum chemical shift for the water line will be excluded from the peak picking.

1H Diagonal

Specifies the tolerance for the identification proton diagonal peaks, for example in a 15N-NOESY-HSQC spectrum. Peaks with equal 1H frequencies within this tolerance are considered to be a diagonal peak and not picked or assigned.

Assignable Spectra

The table lists the assignalble spectra that will be used for the peak picking.

Spectrum

The spectrum name.

Assign Non-root dim?

If set to 'Yes', the higher dimensional peaks will be assigned to a new resonance in the non-root dimensions. For example, in case of a HNCACB that is being picked based on a root 15N-HSQC, the 13C dimension is the non-root dimension.

Experiment Type

Shows the full experiment type of the given spectrum (see also Experiments: Experiment Prototypes).

Dimensions

Shows the dimensions in the spectrum.

Link Peaks

The {Link Peaks} tab provides the interface for the user to pick higher dimensional peaks from the selected root peaks. Depending on the selected options in this tab, selecting a root peak from the Link Peaks table navigates the navigation window to the position of the root peaks that allows easy inspection of the spectrum at that location. Subsequently, the user can decide whether to pick and assign the peaks at that location.

The Assignment: Link Peak Lists popup (Link Peaks).

Navigate to root

Specifies whether to navigate to the root frequencies in the navigation window.

Navigate to targets

Specifies whether to move the marker to the (target) root frequencies in the navigation window.

Set Non-root Atom Types

Specifies whether to automatically set Non-root Atom Types. This option works in the case where there is no ambiguity in the atom type that is observed in the non-root dimension, and then only for the types CO, CA, CB & HA. For example, in a HNCO or HNcaHA spectrum.

Link Peaks table

This table lists the all the root peaks in the root peak list.

#

The serial number of the root peak.

Assign F1, F2...

The assignment information of the peak in given dimension.

Shift F1, F2...

The chemical shift of the peak in given dimension.

Next Root

Selects and navigates to the next root in the list.

Previous Root

Selects and navigates to the previous root in the list.

Assign Root Resonances

Assigns the root resonances of peaks that are within the tolerances of the selected root peak. In some cases the user may want to pick the peaks manually, and add the assignments to root resonances later on using this option. 

Pick & Assign Root Resonances

Automatically picks and assigns peaks within the tolerances of the root peaks. The assignments are made only for the root resonances.

Assign Non-root Resonances

Assigns the non-root resonances of peaks that are within the tolerances of the selected root peak. In some cases the user may want to pick the peaks manually, and add the assignments to non-root resonances later on using this option.

Assign All Root Resonances

Assigns all the root resonances of peaks that are within the tolerances of all root peaks.

Pick All & Assign Root Resonances

Automatically picks and assigns all peaks within the tolerances of all root peaks. The assignments are made only for the root resonances.

Assign All Non-root Resonances

Assigns all the non-root resonances of peaks that are within the tolerances of all root peaks.