Quick User's Guide

Working with NMRView is easier if you understand a couple of key concepts. First, there is what we'll call the working memory. To get data into NMRView, you first "read" spectra, protein sequences, peak lists, etc., yet these initial readings will have no immediately apparent consequence. For something meaningful to happen, you must open a "window," which at first will be blank. Clicking within the window will give you a range of actions you can perform, some of which enable you to bring in data from the working memory. Thus, you can bring one spectrum into two windows by creating two windows and reading the same spectrum into each from the working memory. You can also bring multiple spectra in to one window, and keep other windows open with the individual spectra, if you choose. For simply displaying one spectrum, you can use the "open and draw dataset" option, which brings the spectrum into the working memory, creates a window with the spectrum's name, and draws it in the window. The system is very flexible, and is limited largely only by the number of windows you can tolerate on your desktop. There are also advanced tools within NMRViewJ, like RunAbout, that create a single panel with an organized array of windows inside. These are particularly helpful when analyzing triple resonance data for assigning protein spectra.

If you open multiple windows, you will probably soon discover that they talk to one another. Moving the cursors in one window can move the cursors in the other windows, enabling the spectral positions of the cursors to be the same in all windows. This is a very nice feature when, say, comparing TOCSY and NOESY data to see which peaks are shared in the two spectra.

Most actions in NMRView are effected by left-clicking. Right-clicking and center-clicking are necessary for many essential functions. If you're using a Mac with one button, as you would on a laptop, left-click normally, option-click for center-clicking, and command-click for right-clicking. Or pop for a $15 two-button + center scrollwheel/button USB mouse. In this guide, simple "clicking" without reference to left, right, or center, should be taken to mean "left-clicking.

We've tried to stick to consistent usage for the words "toolbar", "menu", "window" and "panel." In our scheme, a "panel" is an object that appears on the screen into which you can enter text, make choices, effect adjustments, etc. A "window" is an object primarily for display, such as that used for showing spectra. Thus, multiple windows can appear in one panel. A "toolbar" is a row of buttons, usually horizontal, which enable access to menus, which are usually vertical. A toolbar may be its own object on the screen, like the NMRView Main Toolbar (Figure 3.1, “NMRView Main Toolbar”), or a horizontal row of buttons atop a panel. A menu is a simple vertical set of choices that can be selected by clicking; menus are most commonly accessed by clicking toolbar buttons.

Figure 3.1. NMRView Main Toolbar