Resonance : Resonances

A Table of Resonances Organised by Chemical Shift List

This popup window is basically a table of all the resonances that have chemical shifts contained within a selected shift list. This data, in-keeping with the CCPN Resonance entities it represents, serves as the central record that ties atom assignments to peak assignments. An individual resonance many be anonymous and not (yet) carry an atomic assignment but still exists as an entity that carries a chemical shift record and connections to peaks in spectra. Each resonance row in the table may be considered as a “phenomenon number” that may be used to connect various things together when assignments are made. Within a given shift list each resonance will one have only one chemical shift value, but a resonance may have different chemical shift values in separate shift lists, for example corresponding to different conditions; where the resonance phenomenon is the same (from the same atom) but its position in spectra changes.

The resonance table serves both as a source of information in its own right and a means of finding information related to a given set of assignments. For example the user may wish to sort the resonances according to residue sequence (click on the “Residue” heading), scroll to and select the desired residue and then [Show All Peaks] that are associated with the residue assignment. In normal operation the user selects the appropriate shift list (e.g. for the set of conditions) and any isotope, status or molecular subset to fill the table with a series of resonance records. Each resonance is shown with its chemical shift value, any atomic or residue assignment, isotope type and various other useful information. From the table, operations may be performed on a selected subset of resonances by selecting the relevant row; left click +/- <Ctrl>/<Shift>, and then clicking on the buttons.

Navigation

The upper “Navigation & Marks” section allows the user to display resonance positions in the spectrum windows. The user can build strips (sub-divisions) with the selected resonance positions (e.g. selecting H & N amide resonances), center the contour display and create marker lines at the locations. Although similar functionality is also available from the peak table, the user cam get more flexible control by selecting resonances, for example to navigate to a location in a spectrum where a peak is expected, but has not been picked. It should be noted that the [Strip Selected] and [Go To position] functions operate on the spectrum window selected in the “Window” pulldown menu.

Atom Assignment

The penultimate row of buttons represent functions that change the atomic assignment if the selected resonance (or resonances, depending on the operation). Accordingly, a resonance may be disconnected from atoms, linked to atoms, given an atom type (e.g. a general “HA”) and added to or removed from a spin system; a group of resonances belonging to a residue. The last two options relate only to resonances that are deemed to be prochiral, for example like Ser HB2/HB3, which often cannot be distinguished until the latter stages of 3D structure calculation.

General & Information

The lower row of buttons relate to functions that do not involve atom assignment. For example resonances may be deleted; either those that are selected or those that are considered to be “orphans” - without any current assignments to spectrum peaks. The two “Show Peaks” buttons display tables of the spectrum peaks that are currently linked to the selected resonances, optionally considering only spectra that use the selected shift list. The last [Info] button opens the Resonance Info table for the last selected resonance to display the positions of all the peak dimensions to which it is assigned and all its chemical shift values, from multiple shift lists.

Caveats & Tips

The [Delete Orphans] function is commonly used to tidy up projects where there are large numbers of resonances that are no longer assigned to any peaks. This may occur for example resonances have been automatically added to newly picked peaks but once assignment is complete many of the resonances turned out to be duplicate, e.g. separate resonances were initially added to HNCA and HNcoCA peaks even though the resonances should be shared.

If a resonance has a large standard deviation in its chemical shift use the [Info] button to show the peak dimension positions that formed the chemical shift average.

If the list of resonances in the table is too large to easily find a particular resonance, consider using the filtering selections at the top or click the ”?” in the table headings to filter directly on table content.

Main Panel

Selection

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

pulldown Shift List: Selects which chemical shift list to display resonances for, and hence which shift value to use for a resonance. Includes an option to show resonances without any shifts

pulldown Isotope: Selects subsets of resonances to list, according to their isotope type

pulldown Status: Selects subsets of resonances to list, according to their assignment status

pulldown Chain: Allows restriction of the resonance list to only those assigned to a given molecular chain

pulldown Residue Code: Allows restriction of the resonance list to only those assigned toa particular kind of residue

Resonance Table

The main table displaying the resonance records in the selected shift list, and considering filtering options

Table 1
# The serial number of the resonance in the NMR project
Shift The chemical shift value of the resonance in the selected shift list (Editable)
SD The standard deviation in the chemical shift value for the resonance
Assign Name The name bestowed upon the resonance by virtue of its atomic assignments
Residue The residue to which the resonance may be assigned
Isotope The type of isotope responsible for the resonance
Other Name A user-editable name for the resonance, often displayed if atom assignments are absent (Editable)
All Peaks The total number of peaks assigned (via their dimensions) to a resonance (Editable)
Shift List Peaks The number of peaks assigned to a resonance, considering only the selected shift list (Editable)
Spin System # The serial number of the spin system in which the resonance resides

Atom Assignment

Functions to change how the selected resonances are assigned to atoms

button Deassign: Remove any atomic assignments from the selected resonances

button Assign: Assign or re-assign the last selected resonance to atoms (opens the atom browser)

button Set Atom Type: Set the assignment type of a resonance by selecting a representative atom

button Add to Spin System: Add the last selected resonance to a spin system grouping, if not already in one

button Remove from Spin System: Remove the selected resonances form any spin system grouping

button Swap Prochirals: If the last selected resonance is a prochiral, swap its atom assignment for the other stereochemical option

button Ambiguate Prochirals: For the last selected resonance, make any unambiguous prochiral assignment ambiguous, i.e HB2 -> HBa/HBb

General & Information

General functions to administer resonances and get connected peak information

button Delete: Delete the selected resonances form the CCPN project

button Delete Orphans: Delete all resonances that have no assignments to peaks

button Merge or Split: Merge multiple resonances & any peak assignments into one. For a single resonance split into two duplicate resonances

button Show All Peaks: Show a table of all the peaks to which the selected resonances are assigned

button Show Shift List Peaks: Considering only the selected shift list, show a table of peaks to which selected resonances are assigned

button Info: Show a table of information for the last selected resonance, including a list of all peak dimension positions

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