Organising Windows and Spectra

CCPNmr does not give you one window per spectrum. Instead it gives you windows with set x-y or x-y-z axes (e.g. 13C-13C or 13C-15N-13C or 13C-13C-15N). All spectra which contain those axes are then displayed in that window. Using the Spectra tab at the top of each window you can switch individual spectra on and off. However, you are not limited to the number or type of windows that you have. You can use this in order to organise, group and optimally display your spectra.

For instance, I will often often create a second 13C-13C window for my carbon-carbon correlation spectra. The first I will set such that I can see the aliphatic region and the second so that I can see the carbonyl region. In order to duplicate a window go to Window in the Windows menu, select the window you want to duplicate and click on Clone.

In some cases you may find that Analysis is overlaying spectra which you don’t really want to overlay. For instance, you might like to display your NCACX spectra in a 13C-13C-15N window. Because the x and y dimensions are both 13C, Analysis will also place all your carbon-carbon correlation spectra into this window. I find this unhelpful and prefer not to have all my carbon-carbon correlation spectra visible in the Spectra toolbar of my NCACX window: it unnecessarily clutters the toolbar and makes it is hard to find the NCACX spectra. You can remove the carbon-carbon correlation spectra from the window and from the toolbar by going to Window in the Windows menu and then selecting the Spectra & Peak List Mappings tab. Right at the top you can select the relevant window. In the top part of the pop-up you will then see all the spectra which can be mapped into that window (and in the lower part the corresponding peak lists). Simply make sure that the columns Spectrum In Toolbar, Pos. Contours Visible, Neg. Contours Visible and Slice Visible are all set to No for those spectra which you do not want to see in that window.

For 3D and higher dimensionality spectra it is useful to view different planes of your spectrum. When you read in a 3D spectrum, Analysis will simply create a default window, e.g. a 13C-13C-15N window for an NCACX. You can create a second window with 13C-15N-13C axes in order to see the 13C-15N plane rather than the 13C-13C plane of the spectrum. Go to New Window in the Windows menu. Give your new window a name and at the top select the axes you want. If you want to exclude certain spectra from the toolbar from the start, then make sure that these spectra have a No in the In Toolbar? column. If there are a lot of spectra which are mapped to the window and they are all visible, it can take a long time for Analysis to draw all the contours. So it is often better to select all spectra and click on Selected Not Visible (once the window has been created you can switch the spectra back on using the Spectra toolbar). Finish by clicking Create Window!.