Resonance : Spin Systems
Tabular Displays of Resonance Groups
This popup window is used to display tables of the spin systems within a
project, from these the user can perform various residue-level assignment
and navigation operations and follow links to several kinds of relevant
information, like peak and resonance information. In CCPN parlance a “spin
system” is a grouping of resonances that relate to a residue or part
residue. Typically in an assignment project you might start with a spin
system that consists only of amide 1H and 15N resonances and then add side
chain resonances like CA & HA. Such a grouping of resonances relates to the
atoms within a given residue, but the identity of the residue need not be
known before a spin system is generated. Accordingly, a spin system may be
completely anonymous. As more information is gained the spin system could
be allocated a residue type, and then finally a sequence position.
The various tabs of this popup break the spin system information into
several sections, with the aim of avoiding clutter, but the underlying spin
system entities represented in all the tables is the same and all carry an
indication of the current assignment status. The differences are only a
matter of presentation. Selections made in any of the spin system tables
dictate which are used for the upper “Display” buttons or the lower panel
of buttons. The four tables sub-divide the spin system information as
follows:
- The “Assignments” tab lists the names of the individual resonances that are
grouped by each spin system. Also the user is able to set a name for the
spin system, shich will be displayed on spectra in the absense of any
residue assignment information.
- The “Seq. Links” tab is used to display how spin systems have been
connected as sequential neighbours. Such links are independent of a
full residue assignment, and usually derive from the peak matching
performed by tools like the Protein Sequence Assignment option.
Often spin systems are connected as sequential neighbours before
they are fitted into a protein chain to give the final residue assignment.
- The “Shifts” tab displays the chemical shifts of the resonances that are
contained by each spin system. The actual values displayed come from the
from shift list selected at the top.
- The “Details” tab allows the user to make verbose textual comments for
each spin system. This is particularly useful for recording thoughts that
relate to assignment possibilities.
Button Functions
The various functions available as buttons operate on the spin system (or
spin systems where appropriate) that have been selected in the current
table; using left mouse click +/- <Ctrl>/<Shift>. The “Display” functions
at the top are designed to locate the selected spectrum window so so that it
displays the resonances positions from the selected spin system, although
only appropriate resonances are used according to axis/isotope type and
spectrum width. In this way the user can find amide strips in an HNH window
or HC strips in a HCH window. The “Display Cells” option is the same as the
“Display Strips” option in most regards but differs in that the strips are
sub-divided into cells, if resonances from the spin system are visible on
that axis. This is handy to show the points of resonance intersection,
e.g. for amino acid side chain assignment.
The various Assign/Deassign buttons naturally control how a spin system is
linked to residue information. Assignments may be made (or broken) to
specific residues, residue type only or in a tentative/speculative manner.
Although these functions are often handy, spin systems will automatically
be assigned to the relevant residue if one of the contained resonances
is assigned elsewhere to a specific atom in a residue; typically
residue assignments are make when resonances are assigned to atoms
via the Assignment Panel.
The “Show” functions are used to show tables of the spectrum peaks and
resonances that connect to selected spin systems, and from these the user
may then navigate within spectrum windows and perform assignment from these
other contexts.
Caveats & Tips
If a shift appears to be missing within a spin system I could be that a
resonance is simply not assigned in an experiment that uses the selected
shift list, in this instance there may be a shift in a different list.
To expedite finding particular spin systems within a large table the user
can filter the display to only particular spin system types using the
“Status” pulldown menu at the top. Alternatively the user can click on a
”?” in the headings of a column to filter the table rows according to a
user-specified value.
Main Panel
Status: Selects which kind of spin system to show, according to its assignment status
Shift List: Selects which shift list the displayed chemical shift values are from
Filter table rows by Shift List: Whether table resonances and rows are filtered by Shift List for Assignments and Seq. Links tabs
Clone: Clone popup window
Help: Show popup help document
Close: Close popup
Display Strips: Use the resonances in the selected spin systems to define positions for building strip panels in the selected spectrum window
Display Cells: Use the resonances in the selected spin systems to define positions for building resonance intersection cells in the selected spectrum window
Window: Documentation missing
Assignments
A table listing all the spin systems within the project, including the names of all contained resonances
Table 1 |
# |
The spin system serial number |
Chain |
The code of the molecular chain to which the spin system is assigned |
Residue |
The sequence number and name of the residue to which the spin system is assigned (Editable) |
Other Name |
A user editable name for the spin system; displayed in spectra if there are no residue assignments (Editable) |
Resonances |
The complement resonances that are present within the spin system (Editable) |
Num Peaks |
The number of peaks is the project to which the spin system’s resonances are assigned |
Seq. Links
A table listing spin systems and any sequential connections they nay have
Table 2 |
# |
The spin system serial number |
Chain |
The code of the molecular chain to which the spin system is assigned |
Previous |
The residue linked as being one position before the spin system in chain sequence |
Current |
The sequence number and name of the residue to which the spin system is assigned |
Next |
The residue linked as being one position after the spin system in chain sequence |
Backbone Resonances |
The names of the assigned backbone resonances within the spin system (Editable) |
Seq. Segment |
For sequentially connected runs of spin systems, the number of the run and the position within the run at which the spin system is found (Editable) |
Shifts
A table listing all of the chemical shift values of the spin systems within the project
Table 3 |
# |
The spin system serial number |
Chain |
The code of the molecular chain to which the spin system is assigned |
Residue |
The sequence number and name of the residue to which the spin system is assigned (Editable) |
Unassigned |
The chemical shifts of the resonances in the spin system not assigned to atoms |
Details
A table listing allowing verbose textual comments for each spin system
Table 4 |
# |
The spin system serial number |
Chain |
The code of the molecular chain to which the spin system is assigned |
Residue |
The sequence number and name of the residue to which the spin system is assigned (Editable) |
Details |
A verbose user-editable textual comment for the spin system (Editable) |
Residue: Assign the last selected spin system, and the resonances it contains, to a specific residue in a molecular chain
Tentative: Assign the last selected spin system, and the resonances it contains, in a fuzz or putative manner to a specific residue
Type: Assign the residue type of the spin system; selecting any residue of the required kind
Residue: Removes the specific residue assignment form the selected spin systems, any contained resonances will be deassigned too, but will still carry atom type information
Tentative: Removes any fuzzy or putative residue assignment from the selected spin systems
Type: Removes any residue type information from the selected spin systems
Merge: Merge the selected spin systems into one; all contained resonances will be put in the same group and the last selected spin system will have any overriding assignment
Delete: Delete the selected spin systems; only allowed if the have no resonances, show and unlink resonances if cleanup is required
Show Peaks: Show a table of the peaks assigned to the resonances of the selected spin systems
Show Resonances: Show a table of the resonances contained in the selected spin systems
Predict Type: Open a tool that predicts the residue type of the last selected spin system, based on the chemical shift values if its resonances
New Spin System: Make a new, blank spin system, into which resonances may be placed