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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 compund, because each experiment provides its piece of information. It is convenient to coordinate the whole information. In this way, when you assign a resonance to an atom, the same information is automatically available (and displayed) in all the experiments. The coordinating document, repository of resonances and cross-peaks, is called “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 can be slightly different from the average frequency of the resonance.

How to Initialize a Cross-Peaks Manager (CPM):

Step 1

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 well-known equivalents. The manager interface is a tiny window that floats over the document windows. It only contains two menus and three switches (to show or hide assignments, resonances and cross-sections).

Step 2

The menu at the left (“Experiments”) contains a list of the managed experiments. You can add them when needed, one by one, or altogether from the start. 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 into the Experiments menu. iNMR requires the tags but ignores their meaning, they are only for your convenience. Close the dialog.

Step 3

You can already save your manager, even if it's empty. It is convenient to store both the manager and the managed experiments into the same folder. If, in future, you move one of the files, the other files must be moved together, otherwise the connections are lost. Never save, however, the CPM inside the same folder that already contains a “fid” or “ser” file. Save it just outside that folder.

Step 4

The exp. 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).

Step 5

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 the name of the atoms corresponding to the vertical and horizontal frequencies. You can optionally indicate a name for the residue (or group; for example, the name of the aminoacid, if your compound is a peptide).

Step 6

You can use the peaker tool to select a region: iNMR will automatically create anonymous assignemnts for the selected peaks. If, instead, you select an ensamble 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.

Step 7

To modify an assignment (reassign a peak), click on 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 on the big X (Y) on the left, then click on 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.

Step 8

Select another experiment from the exp. 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.

Step 9

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 shows the list of resonances. You can change the name of a peak or of a group. The change will affect all the related cross-peaks. When an assignment is deleted, the corresponding resonances usually survive to it. You can delete them inside 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

Cross Peaks Manager Commands

Changing the Font

Integrals by Volume-Fitting

Arrays of Bidimensional Experiments

Keyboard Commands to Manipulate a 2-D Plot

Exporting to Other Programs