Peak : Selected Peaks

Show a Subset of Peaks in Tabular Form

The idea behind this table is to give a textual listing of a particular subset of peaks. This table may be shown in two separate contexts; to represent all the peak entities which may be selected in one or more spectrum window displays inside Analysis, or it may be used by the various [Show Peaks] functions inside Analysis. When used for the display of in-spectrum selections, this table may be opened from the main Analysis menu or via the “Peak::Selection Table” option of the right-click window (shortcut is “s”). Also, the contents of this table changes as the selected peaks change, thus representing the current selection status.

The listed peaks may be from several different spectra of any dimensionality or type. Putting the peak selection into a table of this kind allows the user to make easy comparisons and editing of their parameters, e.g in terms of assignment or intensity, and also provides links to other kinds of information. For example the user can go from the selected peaks to the resonances that are assigned to those peaks. Double-clicking on the editable columns of the table allows many of the parameters to be directly edited, although discretion is recommended for certain operations like changing positions and intensity values.

Spectrum Window Navigation

The options above the peak table provide functions that allow the user to locate and mark peaks within the spectrum display windows. The [Strip Selected] and [Find Peak] options are used to find particular peaks that have been selected in the table (with left-click +/- <Ctrl>/<Shift>). The former sub-divides the locations for separate peaks using strips (window dividers) and the latter locates only the last selected peak. The [Strip Locations] and [Go To Position] work in a similar way, except that they use only the position information from the selected peaks and don’t necessarily display the actual selected peaks. The idea here is that peak positions can be used to move the display of any spectrum window that share at least some of the same kind of isotopes on their axes. For example a 2D 15N HSQC peak can be used to find an amide position (H & N) in 3D HNcoCA spectrum, thus locating two out of three axes. This functionality is very useful when some peak lists are used as “roots” to coordinate others.

Button Functions

The buttons below the main peak table allow the user to edit and view many types of data associated with the peaks, although many parameters may be changed by double-clicking in the peak table. Some notable functions include: [Unalias] which is used to move ‘ghost’ peaks to their real underlying ppm values by adding or subtracting a whole number of spectrum widths to their position. This is used when a peak lies outside the normal recorded bounds of the spectrum but nonetheless still appears within it because as an aliased signal; [Assign] opens the Assignment Panel to control which resonances have been linked to the dimensions of the peak; to indicate what caused the peak. Such assignments may be to the resonances of specific atoms or resonances that are currently anonymous; [Deassign] clears all of the resonance assignments to the peak dimensions. This does not affect how the resonances may be connected to atoms; [Set Details] allows the user to set the “Details” column for all of the peaks selected in the table with a single operation; [Propagate Assign] spreads resonance assignments from one peak (the last selected) to the others selected in the table, which is useful even if not all of the peak dimensions are the same type, for example when spreading amide H & N resonances from an HSQC peak to 3D triple-resonance peaks.

Caveats & Tips

If you need the peak positions to be displayed in Hz units or as data point positions, the “Position Unit” pulldown at the top may be changed.

The [Set Details] function can be handy for marking peaks that cause violations in a structure calculation and thus need further attention.

Main Panel

button Strip Selected: Use the positions of the selected peaks to specify strip locations in the selected window

check Find Peak: Locate the currently selected peak in the specified window

pulldown Window: Choose the spectrum window for locating peaks or strips

check Mark Found: Whether to put a cross-mark though peaks found in a given window

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

button Strip Locations: Use the selected peak positions to specify strip positions in a higher dimensionality window.

check Go To Position: Use the selected peak position to navigate to a location in a higher dimensionality window

pulldown *None*: Choose the higher dimensionality spectrum window to use as a navigation & strip target

button Mark Selected: Put multidimensional cross-marks through selected peaks

pulldown Position Unit: Choose whether to display peak positions in ppm, Hz or points

Table 1
Spectrum Experiment:spectrum of peak
List Peak list number
Peak Peak serial number
Height Magnitude of spectrum intensity at peak center (interpolated), unless user edited (Editable)
Volume Integral of spectrum intensity around peak location, according to chosen volume method (Editable)
Merit Figure of merit value for peak; zero: “bad” one: “good” (Editable)
Details User editable textual comment for peak (Editable)
Fit Method Method used to fit the peak location (Editable)
Vol. Method Method used to calculate the peak volume integral (Editable)

button Add: Add a new peak, specifying its position

button Edit: Edit the position of the currently selected peak

button Unalias: Move the ppm position of a peak a number of sweep withs to its correct aliased/folded position

button Delete: Delete the currently selected peaks

button Assign: Assign the dimensions of the currently selected peak

button Deassign: Remove all assignments from the currently selected peaks

button Set Details: Set the details field of the currently selected peaks

button Set As Current: Set the peaks selected in the table as the ones selected in the spectrum windows

button Resonances: Show a table of resonances assigned to the selected peaks

button Deassign Dim: Deassign a specified dimension of the selected peaks

button Recalc Fit: Recalculate the center, height and line width of the selected peaks

button Recalc Volume: Recalculate the volume of the selected peaks

button Show On Structure: Show the assignment connections of the selected peaks on the selected structure

button Propagate Assign: Spread the resonance assignments of the peak last selected to all selected peaks

button Propagate Merit: Copy the merit value of the last selected peak to all selected peaks

button Propagate Details: Copy the details of the last selected peak to all selected peaks

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