Window

Introduction

Window popups, or spectrum windows, are the main user interface to view and interact with NMR spectrum data, and an Analysis project may contain an almost limitless number of spectrum windows. The windows are inherently N-dimensional with scrollbars for not only the screen dimensions but also for orthogonal planes, with the ability to select any plane thickness. A window can be divided into several strips for easy comparison of different regions of spectra.

Multiple spectra can be superimposed in the same window where their contours and peaks are readily toggled on or off. Navigation is achieved by using the mouse or keyboard and there are inbuilt navigation functions to easily find orthogonal planes and return-peak positions.

The Window menus, which are accessible from the right mouse button allow the user to perform a variety of actions on the window itself, or on selected peaks in the spectrum window. For example peaks may be assigned, deleted, unaliased and shift matched. Several of these functions can be used on several peaks at once to improve user efficiency. For example, columns of NOE peaks derived from the same amide resonances may be assigned to this amide at the same time.

Spectrum windows can be created and edited with the Windows: New Window and Windows: Edit Windows popups, respectively.

Window basics

A spectrum window consists of several attributes that provide user interaction tools and information. The number of attributes and their options depends on the dimensionality of window and the spectra associated with the window.

The basic attributes of a spectrum window.

The main attributes are:

• • The spectrum frame, in which spectrum contours, peaks and their annotations are displayed. The spectrum frame can be subdivided into strips, either vertical or horizontal, to display different parts of the spectrum simultaneously (see below).

  • The main toolbar, which in the basic form consists of the toolbar buttons

    • • [Spectra]

      • [Contour]

      • [Peaks]

      • [Strips]

  • which each cause the expansion of the toolbar with additional functions specific for the main toolbar buttons (see below).

  • Side traces, which show 1D traces of the spectra at the current cursor positions. Side traces can be shown/hidden by using the  Window menus Window option, or from the Windows: Edit Windows popup. Within a side trace a right mouse click shows another window menu: Reference, which opens the Set spectrum referencing popup.

  • The size (or height) of the side trace and the height of the spectrum traces can be set in the Windows: Edit Windows popup, by respectively modifying the |Side Trace Height| and |Slice Range| in the {Windows and Axes} tab. The size (or height) of the side trace can also be set by modifying Slice size parameter in the Window menus Window menu.

  • Scroll bars, which allow the user to navigate through the spectrum view in each dimension of the window. Scroll bars can be displayed for each dimension: X, Y and the orthogonal dimensions Z1, Z2 etcetera. Scroll bars can be shown/hidden by using the  Window menus Window option, or from the Windows: Edit Windows popup.

  • Cursor position, which displays the coordinates in X and Y of the current cursor position.

  • Cross hair, which can be displayed for user convenience. Showing or hiding cross hairs can be done in the Edit Analysis Profiles popup.

Spectra

The [Spectra] button adds the Spectra toolbar to the main toolbar, which consists of buttons for each of the spectra defined in the window. Toolbar buttons of currently displayed spectra are highlighted. 

The spectrum window popup (Spectra).

Contour

The [Contour] button adds the Contour toolbar to the main toolbar, which allows the user to modify the contours of the currently displayed spectra in a variety of ways:

The spectrum window popup (Contour).

Peaks

The [Peaks] button adds the Peaks toolbar to the main toolbar, which consists of buttons for each of the peak lists associated with the currently displayed spectra. Toolbar buttons of currently displayed peak lists are highlighted. The option Multi-list allows the user to toggle between the possibility to display only a single peak list, or multiple peak lists simultaneously. 

The spectrum window popup (Peaks).

Strips

The [Strips] button adds the Strips toolbar to the main toolbar, which allows the user to create and modify multiple views (strips) in the spectrum frame:

• • adds a new strip to the window

Inactive strips are shown grey:

The spectrum window popup (Strips).