Loading Projects and Spectra
Open an existing project
Start CcpNmr Analysis on the command line by typing:
-> analysis
(This assumes that the CCPN bin/directory is on your path, otherwise you will need to type the full path or be in the bin/ directory.)
When the Analysis menu bar has appeared select M:Project: Open Project. Navigate to find and then select the CcpnCourse1a project (the directory initially will be in green and then when you have selected it in deep purple). Then click [Open].
You might get a warning that various files have moved location, which is fine; just click [OK]. You might also get a dialogue panel with a list of spectra paths (because those also have moved location). If the paths are all in grey then just click the [All Done!] button at the bottom. If any path is in red then Analysis cannot find the corresponding spectrum data file, so either you need to tell Analysis where it is (by double clicking the path cell and navigating to the correct location) or accept that that particular spectrum will not have its contours displayed.
Now save the new project by selecting M: Project: Save. The first time you save a project that has moved locations the SaveAs dialog 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. For now just hit the "Save" button.
After this 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).
This project has two windows, "window1" and "window2". The first is a two-dimensional window with an HSQC spectrum in it, and the second is a three-dimensional window with two spectra in it, an HNCA and an HNcoCA.
Opening Spectra from File
To open a new spectrum go to M: Experiment: Open Spectra. In the resultant Open Spectra popup navigate to the CcpnCourse1a/spectra/directory and select 182.spc.par (the other three files are the spectra that are already open). You can open up more than one spectrum at one time, but there we will just open one.
If necessary enlarge the popup (click and drag the bottom edge down) so that you can see the entry in the bottom table. This table is a list of how the selected spectra 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 a name for the selected experiment by double clicking on the experiment name cell, "Expt_4", and entering the name and then pressing 'Return' or clicking outside the box. Set the name of the experiment to "N-NOESY" (or similar). The spectrum name could also be altered, but this is not necessary here and the spectrum name being inherited from the spectrum file ("182.spc") is 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 Spectrum].
Now file and referencing verification dialogues will appear. Again, enlarge the popup so you can see the entire table. The {Verify Referencing} tab will be open - it shows the 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. Note that you can change spectrum referencing and file setup at any time after loading via M: Experiment: Spectra.
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 time should 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 experiment that was 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.
Set the synonym for the new experiment to "15N HSQC-NOESY". Note that for this experiment there are two different full types with the same synonym (double click the Full Type column). So 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 experiment the selection H_H[N].NOESY is correct. When the experiment type is set:
, 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. After a few moments you will hopefully see the newly loaded spectrum appear. You can now also close the Open Spectra popup.