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

pulldown Status: Selects which kind of spin system to show, according to its assignment status

pulldown Shift List: Selects which shift list the displayed chemical shift values are from

check Filter table rows by Shift List: Whether table resonances and rows are filtered by Shift List for Assignments and Seq. Links tabs

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

button Display Strips: Use the resonances in the selected spin systems to define positions for building strip panels in the selected spectrum window

button Display Cells: Use the resonances in the selected spin systems to define positions for building resonance intersection cells in the selected spectrum window

pulldown 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

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)

button Residue: Assign the last selected spin system, and the resonances it contains, to a specific residue in a molecular chain

button Tentative: Assign the last selected spin system, and the resonances it contains, in a fuzz or putative manner to a specific residue

button Type: Assign the residue type of the spin system; selecting any residue of the required kind

button 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

button Tentative: Removes any fuzzy or putative residue assignment from the selected spin systems

button Type: Removes any residue type information from the selected spin systems

button 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

button Delete: Delete the selected spin systems; only allowed if the have no resonances, show and unlink resonances if cleanup is required

button Show Peaks: Show a table of the peaks assigned to the resonances of the selected spin systems

button Show Resonances: Show a table of the resonances contained in the selected spin systems

button 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

button New Spin System: Make a new, blank spin system, into which resonances may be placed

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