NMRView is most efficiently operated when it has good default locations in which to look for files of different types. Otherwise, you will need to hunt down your files every time you look for them, wasting lots of time going from directory to directory.
With the current version of NMRViewJ, the most efficient way to organize your data is by setting up a project as described in chapter 7. When not working with a project, however, you can tell NMRView where to look for files of different types by setting its various preferences.
To set these locations, go to the Main Toolbar (Figure 3.1, “NMRView Main Toolbar”) and click "File...Prefs." You'll see this window: (Figure 3.4, “Preferences Panel”)
Click the 'Paths and Filenames Button to get to the paths preferences (Figure 3.5, “Paths and Filenames Preferences”) :
The default paths for NMRView assume your data and related files will be somewhere in the NMRViewJ folder, which for me was "/Applications/NMRViewJ/data," "/Applications/NMRViewJ/peaklists," and others. If you're like me, I keep my data in a location outside my /Applications folder. Indeed, if you're working on a shared computer, you probably can't write to /Applications anyway. So you need to modify your paths to make your usage more efficient. The fastest thing to do is to make a "data" directory in your home folder and keep everything there. For this solution, I would enter "/Users/jkurutz/data" on every line. However, I generally think it's easier to keep data more separated so I don't get a million files in one place. Figure 3.5, “Paths and Filenames Preferences” shows the default paths I entered when setting up to analyze protein G, our standard sample in the U of C Biomolecular NMR Facility.
For this to work, you must check the "Use Paths" radio button so that it says it's "On". Otherwise, NMRViewJ will default to your home directory. If this button is checked, but you don't have a good name for the path, like the one for VNMR files above (Figure 3.5, “Paths and Filenames Preferences”), you'll be shunted to the default directory and you'll have to click your way to where you want to go.
Other Preferences You can set all sorts of other preferences, including those that determine display features like line width and font, but those aren't necessary for the "quick start" part of this guide, and will be covered in a later section.
