Assignment : Assignment Panel
Assign Resonances To Peak Dimensions
The purpose of this popup window is to control the assignment of resonances to
a specific, picked, peak in a spectrum. Such resonances might already be
associated with a specific atom or they could be anonymous, and only
represented by a resonance number e.g. “[123]”.
The general layout of the window is such that you have two tables for each
dimension of the cross peak, i.e. the dimensions are represented as separate
rows. The first column of tables on the left indicate the resonances which
are currently assigned to the peak dimensions. The second column of tables
on the right indicate the resonances that might be assigned to the peak
dimensions; these are usually ordered according to chemical shift closeness
to the peak position in that dimension.
In normal operation to assign the dimension of a peak to a specific resonance
by clicking on one of the resonance row from the right hand table for the
specific peak dimension. If the resonance is not already assigned, it will
appear in the left hand table to indicate that is now assigned. More than one
resonance may be assigned to a peak dimension (e.g. for overlapping or
ambiguous signals) by clicking on another resonance for the same dimension.
Totally new, never seen before, resonances are added to a dimension with the
[<New>] option; the new resonance then gains a chemical shift based on this
peak dimension position.
Clicking on a resonance row in the left hand tables allows you to remove it as
a peak assignment [Clear Dim Contrib] or change the way that the specific
resonance is linked to atoms or residue spin systems. The light blue buttons
toward the bottom will allow you to add specific atomic assignments, atom type
information or tentative assignments. The light orange buttons allow you to
remove atomic and residue/spin system assignments. Double clicking on a
resonance row will open a pulldown menu with some of these options available.
Various options are given to control which resonance assignment possibilities
appear in the right hand tables. Some options show more possibilities, i.e. by
considering wider position-to-shift tolerances or including matches outside of
the current sweep with. Other options restrict the possibilities, usually to
make the selection more relevant to the current situation; you may want only
assignments within a given molecular system (group of chains), within a single
residue, appropriate for an isotope labelling scheme or those that obey
covalent bond relationships of the recorded experiment.
Caveats & Tips
To change the peak that is being assigned in the window move the mouse over
the desired peak in a spectrum window and press the “a” key (lower case).
The experiment:spectrum identity of the peak is indicated at the top left.
Only resonances that are within the chemical shift tolerances (set per
spectrum dimension) will be shown as assignment possibilities. The chemical
shift value used for each resonance is taken from the shift list for the
peak’s experiment.
Resonance and spin system names can be set by double clicking on an assigned
resonance row and selecting the appropriate option from the pulldown menu.
Resonance and spin system names will be annotated in brackets with serial
numbers, e.g. “{123:contamination}[456:aliphatic]”. Names will not be
displayed if there is any atom, residue or type information. Accordingly names
cannot be set here under such circumstances. These names are free text notes
and have absolutely no formal meaning with regards to assignment or molecules.
Distances only appear in the tables if you have an appropriate structure set
at the top and then only if there are through-space transfers in particular
dimensions of the peak’s experiment.
“Assignment Groups” are only used when you wish to specify mutually exclusive
assignment possibilities, e.g. when you have an NOE peak caused by two signals
and only certain assignments go together. Resonances with the same group
number go together and those with different numbers do not mix; so you would
not get an inappropriate distance restraint for example.
Main Panel
Structure: Selects a structure ensemble from which interatomic distances are calculated
Help: Show popup help document
Close: Close popup
Assignment possibilities
Table 1 |
F1 |
The peak dimension number and position (Editable) |
Table 2 |
# |
Row number |
Name |
Resonance name |
Delta |
Difference between peak dimension position and chemical shift |
Shift |
Chemical shift value of assignment |
SD |
Standard deviation of chemical shift |
Dist |
Resonance-resonance distance in structure |
<New>: Make a new resonance object and link to this peak dimension
Table 3 |
F2 |
The peak dimension number and position (Editable) |
Table 4 |
# |
Row number |
Name |
Resonance name |
Delta |
Difference between peak dimension position and chemical shift |
Shift |
Chemical shift value of assignment |
SD |
Standard deviation of chemical shift |
Dist |
Resonance-resonance distance in structure |
<New>: Make a new resonance object and link to this peak dimension
Options
Aliased Possible: Whether to the peak dimension position may be aliased; matching chemical shifts +/- a whole number of sweep widths
Restrict Mol System: Whether to restrict assignment possibilities to only those within a single molecular system (complex)
Intra-residue: Whether to restrict assignment possibilities to only assignments within the same residue
Correlated Dims: Whether to filter the number of assignment possibilities by enforcing that for directly bound dimensions only directly bound resonances are shown
Double Tolerances: Whether to double the normal assignment tolerances for matching peak dim positions to resonance chemical shifts
Assignment Groups: Whether to display information to specify mutually exclusive assignment groups for superimposed/ambiguous assignments
Isotope Labelling: Selects an isotope labelling scheme, if required, to filter the assignment possibilities
0.1: The lower limit for spin active isotope incorporation at an atom site for a resonance to be considered
Assign Resonance: Assign the resonance selected in a peak dimension table to atoms
Set Type: Set the atom type of a resonance selected in a peak dimension table
Tentative Assign: Assign the selected resonance to atoms in a fuzzy or putative manner
Deassign Resonance: Remove atomic assignments from the selected resonance
Deassign Spin System: Remove residue or spin system assignments from the selected resonance
Clear Dim Contrib: Disconnect the selected resonance from the peak dimension it its currently linked to
Set Same Spin System: Set all resonances assigned to the peak dimensions to be in the same spin system
Show On Structure: Show any atomic connectivities on a graphical structure display. If the peak is assigned the assigned connections are used, otherwise potential possibilities are displayed
Show Peaks: Show a table of all the peaks currently assigned to the selected resonance
Merge Resonances: Merge the selected resonance with the others assigned to the same peak dimension
Resonance Info: Show a table of information for the selected resonance, including the shifts of all the peaks it is linked to