Window : New Window

Create New Windows to Display Spectra

This tool is used to make new windows for the graphical display of spectra, which will usually be as contours. It is notable that some spectrum windows will be made automatically when spectra are loaded if there is no existing appropriate window to display a spectrum. However, making new spectrum windows allows the user to specialise different windows for different tasks and gives complete freedom as to which types of axis go in which direction. For example the user may wish to make a new window so that a spectrum can be viewed from an orthogonal, rotated aspect.

A new spectrum window is made by first considering whether it is similar to any existing windows. If so, then the user selects the appropriate template window to base the new one upon. The user then chooses a name for the window via the “New window name” field, although the name may be changed after the window is created. Usually the user does not need to consider the “Strips” section, but if required the new window can be created with starting strips and orthogonal sub-divisions (although these are not permanent). After setting the required axes and spectrum visibility, as described below, the user clicks on [Create Window!] to actually make the new spectrum display window.

Axes

The number and type of axes for the new window are chosen using the pulldown menus in the “Axes” section. The idea is that the user chooses which NMR isotopes should appear on the X, Y, & Z axes. Naturally, X and Y axes must always be set to something, to represent the plane of the screen, but the Z axes are optional. If not required, a Z axis may be set to “None” to indicate that it will not be used. Up to four Z axes may be specified, labelled as “z1”, “z2” etc., and these represent extra dimensions orthogonal to the plane of the screen, which are often conceptualised as depth axes.

It should be noted that the Y axis type may be set to “value”, which refers to a spectrum intensity axis, rather than an NMR isotope axis. Setting the Y axis to “value” and only having the X axis set to an isotope is used to create windows that can show 1D spectra. Such value axes can also be used for 2D and higher dimensionality spectra, to show the data as an intensity graph (a “slice”) rather than as contours.

Spectra

The lower “Viewed Spectra” section lists all of the spectra within the project that may be shown by a window with the selected axes. All spectra with isotopes in their data dimensions that match the isotope types of the window axes can potentially be displayed. This system also allows for displayed spectra to have fewer dimensions than the axes has windows, as long as at least the X and Y axes are present. For example a 2D H-N spectrum can be shown in a 3D H-N-H window, but not a 3D H-H-N.

For spectra that have more than one data dimension of the same isotope, then which data dimension goes with which window axis is not always known to Analysis. Where there is ambiguity, this system will simply map the spectrum data dimensions in order to the next matching window axis. If this mapping turns out to be wrong, then it may be changed at any time via the main _Windows settings; toggling the “Dim. Mapping” of the “Spectrum & Peak List Mappings” tab.

For the spectra listed in the lower table, which may be placed in the new window, the user has control over whether the spectra actually will appear. Firstly the user can change the “Visible?” column, either via a double-click or by using the appropriate lower buttons. By default spectra are set as not being visible in new windows, and the user toggles the ones that should be seen to “Yes”. This basic spectrum visibility can readily be changed by the toggle buttons that appear in the “toolbar” at the top of the spectrum display, so the “Visible?” setting here is only about what initially appears.

The “In Toolbar?” setting of a spectrum is a way of allowing the user to state that a spectrum should never appear in the window, and not even allow it to be toggled on later via the toolbar at the top of the windows. This is a way of reducing clutter, and allows certain windows to be used for particular subsets of spectra. For example the user may wish to put the spectra for a temperature series in one window, but not in other windows used for resonance assignment where they would get in the way. The “In Toolbar” setting can be changed after a window has been made, but only via the main Windows settings popup.

Main Panel

pulldown Template window: Selects which window to use as the basis for making a new spectrum window; sets the axis types accordingly

Strips

pulldown Columns: The number of vertical strips/dividers to initially make in the spectrum window

pulldown Rows: The number of horizontal strips/dividers to initially make in the spectrum window

button Help: Show popup help document

button Close: Close popup

entry New window name: A short name to identify the spectrum window, which will appear in the graphical interface

Axes

pulldown x: Sets the kind of measurement (typically ppm for a given isotope) that will be used along the window x axis

pulldown y: Sets the kind of measurement (typically ppm for a given isotope) that will be used along the window y axis

pulldown z1: Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window z1 axis

pulldown z2: Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window z2 axis

pulldown z3: Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window z3 axis

pulldown z4: Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window z4 axis

Viewed Spectra

Table 1
Spectrum The “experiment:spectrum” name for the spectrum that may be viewed in the new window, given the axis selections
Visible? Sets whether the spectrum contours will be visible in the new window (Editable)
In Toolbar? Sets whether the spectrum appears at all in the window; if not in the toolbar it cannot be displayed (Editable)
Peak Lists The number of peak lists the spectrum contains

button Create Window!: Creates a new spectrum window with the specified parameters

button Selected Visible: Sets the contours of the selected spectra to be visible when the new window is made

button Selected Not Visible: Sets the contours of the selected spectra to not be displayed when the new window is made

button Selected Not In Toolbar: Sets the selected spectra as absent from the window toolbar, and thus not displayable at all

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