Assigning the Cross-Peaks of nD Experiments
The normal practice is to collect not just one, but several 2-D and 3-D experiments of the same compound, because each experiment provides a specific piece of information. It is convenient to manage all this information together. In this way, when you assign a resonance to an atom, the same information is automatically available (and displayed) in all the experiments. The central repository of resonances and cross-peaks is called the “Cross-Peaks Manager”. By a resonance, we mean an atom name and a frequency. By a cross-peak, we mean a relation between two resonances. The frequency of a cross-peak may differ slightly from the average resonance frequency calculated from all related cross-peaks.
How to Initialize a Cross-Peaks Manager (CPM):
- Choose the command “Tools > Cross Peaks M.”. It creates a new empty manager. For existing managers, you will use the command File > Open or its standard shortcut. The manager interface is a small floating window. It only contains two menus and three switches (to show or hide assignments, resonances and cross-sections).
- The menu on the left (“Experiments”) contains a list of the managed experiments. You can add them when needed, one by one, or all at once. To add an experiment, the corresponding window should already be open. Choose the command “Edit This Menu”. The list of open documents appears. Attach a tag to each one. For example: “COSY”, “NOESY”, etc. These are the names that will appear in the Experiments menu. iNMR requires the tags, but ignores their meaning; they are only for your convenience. Close the dialog.
- You can already save your manager, even if it is empty. It is convenient to store both the manager and the managed experiments in the same folder. If, in the future, you move one file, the others must be moved together, otherwise the connections are lost. Never, however, save the CPM in the same folder that already contains a “fid” or “ser” file. Save it just outside that folder.
- The experiments menu now contains the tags you have defined. Select the first experiment you want to analyze. iNMR will leave some room around the plot for the labels you are going to create. This space can be easily resized with the mouse (click and drag the border of the grid).
- Choose the picker tool (command: Tools > Peak-Picker). It is the same tool used for peak-picking. Click on a peak to assign it. iNMR will ask for the name of the atoms corresponding to the vertical and horizontal frequencies. You can optionally indicate a residue or group name (for example, the amino-acid name if your compound is a peptide).
- You can use the picker tool to select a region: iNMR will automatically assign the selected peaks with temporary names. If, instead, you select a set of assignments, you can apply an action on them (like: delete the selected peaks). You can click and drag an assignment, still with the picker tool, if its position is not correct.
- To modify an assignment (reassign a peak), click it with the picker tool. The assignment dialog will appear again, containing the lists of all the resonances defined so far. If the horizontal (vertical) frequency of your peak corresponds to a known resonance, first click the big X (Y) on the left, then click the table row corresponding to the known resonance. The frequency of a resonance is the average calculated over all the cross-peaks associated with it.
- Select another experiment from the Experiments menu. You will find the same lists of resonances. If you select the info tool from the main palette and move the cursor near a peak, it will show you the names of the resonances instead of the usual ppm values.
- The menu “Actions” contains the command “Copy peaks”. It compiles the table of peaks for the current experiment and puts it on the clipboard. You can then paste the table into a spreadsheet or a text document.
Another command from the Actions menu displays the list of resonances. You can change the name of a peak or a group. The change will affect all the related cross-peaks. When an assignment is deleted, the corresponding resonances usually survive it. You can delete them in the resonances dialog. You can also copy the list of resonances and paste them into another cross-peaks manager or into a J manager.
Related Topics
Arrays of Bidimensional Experiments