Start a new project and load the spectra

Start a new project

Start Analysis on the command line by typing:

-> analysis

Once the program has started and the main Analysis menu bar has appeared select M: Project: New. Into the query box that appears enter a name, without spaces, for the tutorial project, e.g. "TrialProject". Then click [OK] or press 'Return'.

Now save the new project by selecting M: Project: Save. The first time you save a project the Project : Save As popup is brought up. At this point you can choose to change the project name and/or the location where the project directory will be saved. The default is that the project will be saved in the directory where you started Analysis.  The project directory is called the same name as your project (e.g. 'TrialProject').

After the first save, M: Project: Save will just automatically save to the existing location. M: Project: SaveAs will let you save your project with another name, or in another location, but will still have the directory name the same as the project name.

It is a good idea to save now and again in case something goes wrong (either with your work or with the code). Save now by pressing [Save], without changing any of the information, and close the save dialog (you can use the red button at the bottom).

Opening Spectra from File

To open some spectra from file go to M: Experiments: Open Spectra. In the resultant Open Spectra popup select three spectrum parameter files to open. Do this by first navigating to the correct directory, where the downloaded tutorial data is saved (probably in a directory called "analysisTutorialData"). Once in the correct directory click on the line in top table corresponding to "5.spc.par", and then whilst holding down the 'Shift' key click on the "7.spc.par" line. This will highlight three spectra to open:

If necessary enlarge the popup (click and drag the bottom edge down) so that you can see three entries in the bottom table. This table is a list of how the selected files will be placed into the CCPN data structure. Each file will be associated with an experiment and a spectrum that are in turn linked to a shift list. For the most part each experiment carries only one spectrum, as will be the case in this tutorial. However, it is possible to have one experiment with several spectra, e.g. when they are processed differently. All the spectra will use the same shift list, as the experimental conditions are the same, so leave that field alone.

Enter names for the three experiments by double clicking on the experiment name rows, e.g. "Expt_1", entering the name and then pressing 'Return' or clicking outside the box. Set the names of the three experiments to "HSQC", "NOESY-HSQC" and "TOCSY-HSQC" respectively. The names of the spectra could also be altered, but this is not necessary here and the spectrum names being inherited from the spectrum file are informative.

Note that the file format option at the top op the popup is set to "Azara", which is correct for the files we will open. If the spectra were stored in a different format (Bruker, Felix, NMRPipe, NMRView, UCSF, Varian or Factorised) this option would have to be altered. Finally, click [Open Spectra].

Now, for each spectrum in turn, the Verify Spectra popup will appear:

Again, enlarge the popup so you can see the entire table. The {Verify Referencing} tab will be open - it shows parameters you normally need to look at. The {Verify File Details} tab lets you edit where and how the file is stored, but this its not normally needed. Click [Commit] on the button at the top of the popup (from either tab) to continue. You will get a warning about the data bit ordering of the file - just click [Yes] here. Note that you can change spectrum referencing and file setup at any time after loading via M:Experiment:Edit Spectra. For the second and third spectra you can toggle the "Is data big endian" option  in the {Verify File Details} tab to on before pressing [Commit] - or you can continue as the first time.

Note that you may skip all the verification steps, if you know your parameters to be correct, by selecting the "Skip verification dialogs" option before you click [Open Spectra]. You can change almost all the spectrum referencing and file parameters at a later stage, if you need to make adjustments. The only thing that you cannot change after a spectrum is loaded are its primary axes; in terms of number and which isotopes they refer to.

Setting Experiment Types

After the verification there is one final popup where you specify the types of the experiments that were run. This information is very useful later on; for example Analysis uses the knowledge of which experimental dimensions correspond to single bond transfers to automatically remove impossible assignment options. For the HSQC spectrum set the category to "through-bond" and the synonym to "15N HSQC/HMQC" or set the full type to "H[N]". Here the synonym is a human readable, but potentially ambiguous, name for the type of experiment whereas the full type is a precise, but often less readable, descriptor. For Bruker experiments with standard pulse program names, Analysis knows how to fill in the Experiment Type. In other situations you need to do it yourself.

Set the synonym for the second experiment to "15N HSQC-NOESY" and the third experiment to "15N HSQC-TOCSY". Note that for these experiments there are two different full types with the same synonym (double click the Full Type column). For example the "15N HSQC-NOESY" could be either H_H[N].NOESY  or H[N]_H.NOESY, with the difference being that the NOESY transfer can come either before or after the HSQC step. For our experiments the selections H_H[N].NOESY and H_H[N].TOCSY are correct.

When the experiment types are fully set according to the figure below, click [Done] at the top right or [Close - All Done] at the bottom. You may have to expand the popup to see the [Done] button. You can now also close the Open Spectra popup.

Next: Spectrum windows