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.
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.
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.
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.
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
Clone: Clone popup window
Help: Show popup help document
Close: Close popup
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
Isotope: Selects subsets of resonances to list, according to their isotope type
Status: Selects subsets of resonances to list, according to their assignment status
Chain: Allows restriction of the resonance list to only those assigned to a given molecular chain
Residue Code: Allows restriction of the resonance list to only those assigned toa particular kind of residue
Navigation & Marks
Options to locate resonance positions in spectrum windows
Strip Selected: Make strips in the specified window using the positions of the selected resonances
Go To Position: Navigate to the selected resonance positions in the specified window
Window: Selects the spectrum window to use for resonance based navigation
Mark Selected: Put multi-dimensional cross marks at the selected resonance positions
Clear Marks: Remove the resonance-located cross marks
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
Deassign: Remove any atomic assignments from the selected resonances
Assign: Assign or re-assign the last selected resonance to atoms (opens the atom browser)
Set Atom Type: Set the assignment type of a resonance by selecting a representative atom
Add to Spin System: Add the last selected resonance to a spin system grouping, if not already in one
Remove from Spin System: Remove the selected resonances form any spin system grouping
Swap Prochirals: If the last selected resonance is a prochiral, swap its atom assignment for the other stereochemical option
Ambiguate Prochirals: For the last selected resonance, make any unambiguous prochiral assignment ambiguous, i.e HB2 -> HBa/HBb