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Copy Resonance Assignments to Different Peak Lists or Molecules
This popup has two separate but related purposes: firstly, to transfer resonance assignments from one peak list to another peak list where the peaks are in similar, but not identical, positions; secondly, to move or duplicate resonances that are assigned to atoms in one molecular chain to another of similar sequence.
Copying Assignments Between Peak Lists
The general idea of the first tab is to select two peak lists, one of which acts as the “source” where resonance assignments are copied from and another to act as the “target” where assignments are copied to. In general both the source and targets peak lists will be from experiments with the same number and kinds of axis. However, it is also possible to copy assignments to a target peak list that is of lower dimensionality than the source. For example you can copy 3D 15N HSQC-NOESY (H,N,H dimensions) assignments to 15N-HSQC (H,N dimensions) or 2D NOESY (H,H dimensions), and in these cases only resonance assignments that go on dimensions common to source and target will be transferred.
The “Source Peaks” table lists all the peaks that assignments may be copied from, together with an indication the number of peaks that are close and the one that is closest. The “Target Peaks” table is updated for an individual source peak when you click on a row of the “Source Peaks” table; to show you details of all the peaks that match in terms of position.
The matching of peak positions is made according to a chemical shift distance measure and only possibilities that lie within the distance threshold are considered. The chemical shift distance is calculated by taking the difference in peak positions for each dimension, dividing each difference by the scale factor for the isotope that appears on that dimension, squaring the differences and taking the square root of their summation. The isotope scale factors, which you can set in the interface mean that differences in dissimilar dimensions can be compared. By default the distances can be thought of in terms as the “1H” equivalent.
If suitable matches are found, resonance assignments are copied between peaks either on an individual basis, by selecting the required target in the lower table and using [Assign Selected Target], or en masse by using the other buttons which process all of the peaks in the list; copying assignments if there is only a single matching target within the distance threshold, or to the closest matching target. When using the process-all functions it is common to start with a very strict/short threshold radius, assign some peaks and then increase the threshold to consider the poorer matching ones.
Copying Assignments Between Molecular Chains
The second tab is used to move resonances’ atomic assignments to a different molecule/chain, while maintaining assignments to peaks. When copying assignments between molecular chains, i.e. the entities with residues and atoms that you assign, the general principle is that you choose one chain as a source, to get assignments from, and another as a target, to transfer assignments to. Chains may have identical sequences, for example when copying assignments within a homodimer, or reasonably different sequences. In the latter case a pairwise sequence alignment is used to determine the initial mapping between source and target residues.
With the chain selection setup, the next task is usually to consider how moving assignments will affect the peaks that the source chain resonances are assigned to. In this regard there are three options and they are all specified on a per-experiment basis (and thus affect that experiment’s spectra and peaks). The first option is to leave an experiment alone (“don’t move”) so that its peaks are not affected at all. The second option is to move to the target, whereby all resonance assignments on the peaks are moved to the other chain. The third option is to duplicate assignments on the peaks so that they are assigned to both the source and the target chains; this makes each peak assigned to double the number of resonances. If a resonance is moved entirely to the target chain (no peaks left at source) then the resonance’s atomic assignment is simply pointed to the different chain. If a resonance remains partly assigned to the original chain, then a new resonance is made and this is the one assigned to the target chain; the old resonance remains on the source chain.
Where residues don’t match exactly between the two chains, any resonances assigned to atoms with no direct equivalent (nothing of the same name) will still be copied across; their spin system will become the target residue, they retain their original atom types, but they will not have full atomic assignments. If the destination residue does not appear correctly in the lower table, the user may change the residue-residue mapping by double clicking in the “Destination” column.
Documentation missing
Source Peak List: Selects the peak list to copy assignments from
Target Peak List: Selects the peak list which will be assigned
Show Already Copied?: Whether to show source peaks in the table whose assignments are already copied
Overwrite Assignments?: Whether to overwrite any existing assignments in the target peak list
Follow Peaks?: Whether to follow the location of peaks in the spectrum window when clicking on a peak row
Only Good Matches?: When selected only source peaks with at least one good target match will be shown, otherwise all source peaks are shown
Consider Aliased?: Whether target peaks could be aliased; position matching can add whole numbers of sweep widths
Follow Window: Selects which spectrum window will be used to navigate to source & target peak positions
0.08: The ppm search radius to match peak positions. Note spectrum dimensions will be weighted by the isotope scale factors
1.0: The scaling factor used to weight ppm distances in 1H dimensions; used in position radius search
5.0: The scaling factor used to weight ppm distances in 15N dimensions; used in position radius search
10.0: The scaling factor used to weight ppm distances in 13C dimensions; used in position radius search
Table 1 | |
# | Serial number of the source peak |
Assignment | Assignment of source peak; which will be copied |
Num. Matches | The number of target peaks that match the source peak within the ppm distance |
Closest Distance. | The smallest, isotope weighted, ppm distance to a target peak |
Best Match | Assignment annotation of closest matching target peak |
Table 2 | |
# | Serial number of target peak possibility |
Assignment | Assignment of the target peak, which may be overwritten |
Distance | Isotope weighted (by scale factor per dimension) ppm distance between source and target |
Assign Selected Target: Copy assignments from the selected source peak to the selected target
Assign All Singly Matched: Process all source peaks and copy assignments to those that match a single target within the search radius
Assign All To Closest: Process all source peaks and copy assignments to the closest matching target peak (if there is one in the search radius)
Documentation missing
Source Chain: Selects the molecular chain from which atom assignments will be copied
Target Chain: Selects the molecular chain which will receive new atom assignments
Table 3 | |
# | Serial number of experiment to consider |
Experiment | Name of experiment to consider |
Operation | Sets whether atom assignments for an experiment will be transferred entirely, duplicated on both chains or left unaltered (Editable) |
Don’t Move: Sets the selected experiments so that their assignments will be left unaltered
Move to Target: Sets the selected experiments so that their assignments will be transferred entirely to the target chain
Duplicate: Sets the selected experiments so that their assignments will be duplicated for both source and target chains
Table 4 | |
Source | The residue from which assignments may be copied |
Source Resonances | The number of resonance assignments currently on the source residue’s atoms |
Destination | The residue in the target chain to which assignments may be copied (Editable) |
Destination Resonances | The number of resonance assignments currently on the target residue’s atoms |
Copy Assignments!: Go ahead and copy assignments between chains using the selected options
Enable Selected: Enable copying of assignments for the selected residues
Disable Selected: Disable copying of assignments for the selected residues