One often has a case where one has atom assignments but they have not been applied to all of your data sets. In this section we describe a tool for assigning all the peaks in a list based on the current assignment table. Note, a closely related alternative is when one has one assigned peak list and one wants transfer assignments to an unassigned list. This is discussed in the next section
To start this process bring up the Peak -Atom Matcher from the menu entry. Choose the peak list that you wish to assign by clicking on the list chooser near the top. Once you choose a list you'll see a series of rows of information, with one row for each dimension.
For each dimension number listed choose the name of the dimension to match. You can set a tolerance to be used for the matching process. If you leave this blank it will default to 0.1 ppm. Sometimes you know that the peaks are all shifted by a certain amount in one or more dimensions from the assigned shift. This might be because of a deuterium isotope effect for deuterated samples, or due to a splitting from residual dipolar couplings. If this is the case enter an approximate value for the expected shift. In the example below the peaks are shifted by the dipolar coupling so we'll enter a shift of about 0.5 ppm to allow for the expected shift in the 15N direction (the spectra are collected at 81 MHz (15N)so the shift is roughly 90.0/81/2.0). Be careful to choose the sign of the offset correctly. The offset value specified is added to the chemical shift of the corresponding peak dimension, before comparison with atom chemical shifts.
The matching algorithm will search for atoms of a specified type that match the chemical shifts of the peaks. Since the experiment here is an 15N HSQC we'll enter hn for the first dimension and n for the second dimension atom names.
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The matching process is started by clicking on the button. The comparison code will then generate a list of atoms of each residue with the specified atom names. Each atom will be compared with the chemical shifts of the each peak in the selected list and a bipartite pattern matching algorithm will be used to generate an optimal matching of peaks and atom.
The table below the control section will be filled in with a list of peaks and their optimal assignment (if one is found within the specified tolerance). The peak column will list each peak identification number. The entity,and atom name columns (hn and n, in. the example) will show the atom that best matches with the peak. The score value is based on the chemical shift deviation between the matched atom and that of the peak positions. Remember that you can click on any column header to sort (ascending or descending) by the values in that column.
Clicking the button will assign each peak to the corresponding atom, but this will only be done for rows where the match button is selected.
The process then, is:
Select Peak List
Choose dimensions, tolerances, offsets and atom names.
Click to match peaks and atoms.
Review scores and deselect any inappropriate matches.
Click to assign selected (match checkbox) peaks to atoms.