Spectrum visualization

Opening a spectrum

You can open a single spectrum via Project > Open Spectra. A new dialog window will open. Choose the proper file format of your spectra (Bruker, NMRView, NMRPipe etc.) and then navigate to the location of the data file.

Select the spectrum (you can also select multiple spectra) you want to open. It will appear in the list of spectra to open at the bottom of the dialog window. It is now a good time to rename the spectrum by double-clicking on Expt_1 and changing the name to something more meaningful (e.g. HN-ubiquitin).

Click on Open Spectrum. A verification window will then open. Make sure this is the spectrum you want to open, click Commit and in the next window, select the appropriate Type Synonym (15N HSQC/HMQC in this example).

Once you have done that (if opening multiple spectra, it needs to be done for each of them), click on Close - All Done and your spectrum will open in a new window.

Bruker data

In the case of Bruker spectra, you only need to reach the root folder of your experiment and CcpNmr will recognize the <expno>/pdata/<procno>/procs folder automatically.

Navigation

You can now navigate through your spectrum using the mouse buttons and keyboard shortcuts. Here is a reminder of the mouse functions used in CcpNmr.

Mouse button	Action
Left	Select peak
Left + Shift	Select peaks in region
Left + Ctrl	Pick peak
Left + Shift + Ctrl	Pick peaks in region
Right	Options menu
Wheel	Drag spectrum
Wheel + Roll	Zoom
Wheel + Shift + Roll	Navigate through planes of 3D spectrum

Spectrum window menu buttons

At the top of the spectra window lies 4 buttons (Spectra, Contours, Peaks and Strips) that give access to various viewing options.

The Spectra button opens the list of spectra currently loaded in the window (named window1 by default - this can be changed via Ẁindow > Windows, double-clicking on the window name and changing it). In order to hide a spectrum, you can click on its name.

The Contours button enable you to adjust the contour levels. The arrows rise, or lower the contour (base level), in a similar way as the e and r keys. The +1 and -1 buttons let you change the number of levels and the Pos/Neg button let you show/hide positive and negative signals. Note that the changes will apply only to the active (displayed) spectra in the current window.

Finally, the More.. button will open another dialog window which enable you to fine-tune the contour parameters.

The Peaks button let you show/hide peaks from the various spectra displayed in the active window.

Finally, the Strips button let you add, remove activate and navigate through strips. This option is very useful when analyzing 3D datasets.

Example of strips

Customizing the colours and the spectra order

The default teal colour proposed by CcpNmr for the first spectrum that you open may not be the most attractive colour. In order to change it, got to Experiment > Spectra, then Display Options tab.

When you have multiple spectra, it is possible to define the order (rank) which they will follow in the stack. To do so, change the Rank number for each spectrum to match to order you want to see them (lower number will bring the spectrum higher in the stack).

Next step

Once your spectrum is loaded, you can start picking peaks.