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Chemical Shifts

Chemical Shifts

Note that this is new for Version 3.1 - in Version 3.0 the Chemical Shifts are handled slightly differently

You may find it helpful to both read the information and watch the video as they describe things in slightly different ways.

Each project always has to contain at least one Chemical Shift List. New projects are given one called default.

The link between Spectra and Chemical Shift Lists

Each spectrum has to be associated with one Chemical Shift List. When you open a new spectrum, it will by default be associated with the first Chemical Shift List in your project (usually the default list). If you double-click on a spectrum in the sidebar to bring up the Spectrum Properties dialog box, you can see in the General tab which Chemical Shift List the Spectrum is associated with. You can also change which Chemical Shift List this is (including creating a new Chemical Shift List) using the drop-down menu.

An alternative way to manipulate the link between a Spectrum and a Chemical Shift List, is to double-click on a Chemical Shift List in the sidebar. This will show you which spectra are associated with this Chemical Shift List and which are not. You can drag spectra between the Not Included and Included boxes to change which spectra belong to that Chemical Shift List (or double-click on a spectrum to move it to the other box). If you only have one Chemical Shift List in your project, you will not be able to exclude spectra from this. If you move spectra out of the current Chemical Shift List, then they will by go into the first Chemical Shift List. You can't move spectra out of the top Chemical Shift List - move them into another one instead.

When you assign peaks in a spectrum, then the NmrAtoms used for the assignment will be added to the Chemical Shift List of that spectrum. The Chemical Shift value for any one NmrAtom will then be automatically averaged over all the Peaks it has been assigned to in Spectra which are linked to that Chemical Shift List. We refer to these Chemical Shifts as being dynamic because they change dynamically as you assign and deassign peaks in the linked spectra.

If a Chemical Shift for a particular NmrAtom was added to a Chemical Shift List, but later the assignment is removed (i.e. the NmrAtom is no longer being used for any peak assignments), then the Chemical Shift remains in the list, but it is marked as being orphaned because it no longer has a link to any peaks. It's Chemical Shift value is simply the last value it had. Note that when you export a NEF file from your project you can choose whether or not to include ChemicalShift orphans. Usually you will not want to export these as they are often simply the remnants of incorrect or temporary assignments. You can remove all your orphaned Chemical Shifts in one go by going to Macro / Run CCPN Macros / deleteOrphanedChemicalShifts. (Go to Macro / Open CCPN Macro... and select to view or edit this macro.)

When should I use multiple Chemical Shift Lists?

You should use additional Chemical Shift Lists any time you add spectra to your project which are recorded under different conditions resulting in (potentially) changed chemical shifts. So if you record some spectra at a different temperature, a different pH or including different concentrations of a ligand or binding partner, then you should use a different Chemical Shift List. So for a titration, each of your spectra should (ideally) be in a separate Chemical Shift List. Otherwise, your Chemical shifts will be averaged across all the spectra in the titration. If you did not put them in different Chemical Shift Lists, the chemical shifts of the peaks that move will contribute towards the chemical shift of that NmrAtom. And when you go to deposit your chemical shifts in the BMRB, some of them might be distorted!

Duplicating and Importing Chemical Shift Lists

You can duplicate a Chemical Shift List by right-clicking on it in the sidebar and selecting Duplicate. This will give you a snap-shot of your Chemical Shift List at that point in time and because the List isn't associated with any spectra, the Chemical Shifts in it won't change as you manipulate the peaks in your spectra. We refer to the chemical shifts in such a list (which doesn't have any spectra associated with it) as being static because they won't change.

In a similar way, you can import a Chemical Shift List from a BMRB NMRStar or NEF file and then that Chemical Shift List will also not be associated with any spectra and have static Chemical Shifts.

If you later associate a spectrum with a Chemical Shift List of this type, then chemical shifts all become dynamic as they can now be automatically altered through peak assignments and deassignments.

Dynamic, Static and Orphaned Chemical Shifts

Dynamic Chemical Shifts are in a Chemical Shift List which is linked to at least one spectrum. Static Chemical Shifts are in a Chemical Shift List which is not linked to any spectra. A dynamic chemical shift is orphaned if its NmrAtom is not used for any peak assignments in the linked spectra.

If you would like to see whether your Chemical Shifts are dynamic or static or if any of your dynamic Chemical Shifts are orphaned, you can open a Chemical Shift Table (drag it into the Drop Area from the sidebar, or right-click in the sidebar and select Open as Module) and then right-click on a column heading and select Column Settings.... You can then select to view the State and Orphaned columns to see if your Chemical Shifts are dynamic or static. A tick in the Orphaned column indicates that a dynamic Chemical Shift is orphaned. You may delete orphaned or static chemical shifts, but not dynamic one which have peak assignments.

Merging Chemical Shifts / NmrAtoms

You can't technically merge two Chemical Shifts, but you can merge the NmrAtoms that they are associated with. The Chemical Shift List table is a useful place to do this. Simply select any chemical shifts/NmrAtoms wich you would like to merge while holding down the Ctrl/Cmd key to enable multi-selection, then right-click on the chemical shift/NmrAtom that you want to merge the other ones into. Select Merge NmrAtom into NmrAtom X. Note that you can only merge NmrAtoms which have the same Isotope Code.

Chemical Shifts and NmrAtoms

A Chemical Shift can only exist in the context of an NmrAtom, i.e. each Chemical Shift has to have a single NmrAtom associated with it (the NmrAtom is the label for the Chemical Shift and you can't have a Chemical Shift without a label). This means that if you import a ChemicalShift list which contains NmrAtoms/labels which don't already exist in the project, they will be automatically created. It also means that if you delete any NmrAtoms (or NmrResidues/NmrChains) which have Chemical Shifts associated with them, the Chemical Shifts will be deleted at the same time (and any peaks assigned to those NmrAtoms will be deassigned).

Overview Diagram

This diagram shows the relationships between the various objects in the program.

From this you can infer certain behaviours. For example, this is what will happen if you delete any of these objects:
ChemicalShiftList: All the ChemicalShifts in a ChemicalShiftList will also be deleted. You cannot delete a ChemicalShiftList which has Spectra associated with it (to avoid any ambiguity about which alternative ChemicalShiftList these Spectra would then become associated with). Before deleting a ChemicalShiftList, move its Spectra into a different ChemicalShiftList. The final ChemicalShiftList in a project cannot be deleted.
NmrAtom: Any associated ChemicalShifts are also deleted. Any assigned Peaks are deassigned.
Peak: No other objects are deleted. NmrAtoms may become unused and their ChemicalShifts may become orphaned, but that doesn't matter.
PeakList: All the Peaks in the PeakList are also deleted (which can again lead to NmrAtoms becoming unused or ChemicalShifts becoming orphaned). If the PeakList is the only PeakList of a Spectrum, a new empty one is created in its place.
Spectrum: All PeakLists and Peaks belonging to the Spectrum are also deleted (which can again lead to NmrAtoms becoming unused or ChemicalShifts becoming orphaned).
ChemicalShift: If the NmrAtom belonging ot the Chemical Shift IS NOT assigned to any Peaks belonging to the same ChemicalShiftList as the ChemicalShift (i.e. if the Chemical shift is either static or an orphan), then no other objects are deleted. If the NmrAtom belonging ot the Chemical Shift IS assigned to any Peaks belonging to the same ChemicalShiftList as the ChemicalShift (i.e. it is dynamic and not orphaned), then it cannot be deleted.