Users are generally quite familiar with data relating to peaks and atoms, but less so with resonances. NMRViewJ now has a table to display and manipulate some key properties of resonances and their relationship to peaks and atoms. The Resonance Table is accessible from the menu item in the Menu. The columns in the table are as follows:
- id
A number that uniquely identifies each resonance.
- label
A textual label describing the resonance. This is normally set when you enter a label value for a peak dimension. Labels are typically set in the Peak Inspector, by means of some script such as those used in RunAbout, or directly with the nv_peak elem dimNum.L command. Any resonances linked to that dimension will receive that label (actually the the label really only exists on the resonance itself, setting the peak label sets the corresponding resonances label. That way all peak dimensions linked to the same resonance have the same label). There are no constraints on what the label is, but generally it is a good idea to stick to the residue.atomName convention. That makes it easier to actually assign the resonance to an atom at a subsequent step of analysis. The label field can be empty (and initially is for a new resonance).
- atom
The atom that the resonance is assigned to. This will appear as the formal "fully qualified" name of the atom, thus specifying a specific atom (even in a multi-component molecular system).
- peak
One of the peaks that the resonance is linked to. A given resonance can be linked to multiple peaks so the choice of what peak to show here is somewhat arbitrary, though it is done in a way that resonances linked to peaks of the same lists, will show a peak of the same list. A pop-up table showing all the peaks linked to the resonance will be available in a subsequent version of NMRViewJ.
- dim
The label for the peak dimension to which this resonance is linked (as multiple peaks linked to one resonance could have different labelling schemes, the label shown is that from the peak given in the previous column).
- npeaks
The number of peaks that are linked to this resonance.
- ppmavg
The average value of the chemical shift of all the peaks that are linked to this resonance.
- ppmdev
The standard deviation of the chemical shifts of all the peaks that are linked to this resonance.
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As can be seen in the figure above there can be multiple resonance that have the same label. This is entirely dependent on how you (or some script) entered labels for the peaks. Clicking the button will merge together all resonance that have the same label. The atom assignment must be the same for any of the resonances that already have an atom assigned. Furthermore, the chemical shift of the resonances must be similar. After merging the data illustrated here the table looks like this. You can see that resonances 7666, 7915, and 9259 (all with label 54.CA) have been merged with resonance 9106 (also with label 54.CA and atom 54.CA).
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In the above table you can see that there are still resonances, like 52665, that have a resonance label, but no atom label. Clicking the button will search through all resonance like this, and if the resonance label uniquely identifies an atom in the current molecular structure, the resonance will be assigned to that atom as shown here.
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Peak lists may be derived from datasets collected under a variety of different conditions. You may want to view the chemical shifts for given resonances averaged peaks from only a certain set of experiments. In NMRViewJ you can assign a condition label to each peak list in the Peak Reference dialog. Click the menu arrow to the right of the Condition field and choose to get a input dialog in which you can enter a name for a condition. At present these are just names (without an associated set of parameter values).
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Having assigned a sample condition to one or more peaks you can choose that condition in the Resonance Table. All resonances are still displayed but the peak shown, number of peaks and the chemical shift average and standard deviation are derived only from peak lists with that condition label.
You can change the chemical shift that is assigned to atoms by clicking the button. This will scan the resonance list for any resonances that have assigned atoms (not just labels) and set the chemical shift of that atom to the average of all the values of the corresponding dimensions of peaks linked to that resonance. By using different conditions you can set the chemical shifts of the atoms to values found in the different conditions. The underlying code of NMRViewJ allows atoms to have multiple chemical shift values, but we have not yet provided easy access to that information via the GUI. At present, therefore, using this command will replace the "default" chemical shift of the each atom.
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