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
Template window: Selects which window to use as the basis for making a new spectrum window; sets the axis types accordingly
Strips
Columns: The number of vertical strips/dividers to initially make in the spectrum window
Rows: The number of horizontal strips/dividers to initially make in the spectrum window
Help: Show popup help document
Close: Close popup
New window name: A short name to identify the spectrum window, which will appear in the graphical interface
Axes
x: Sets the kind of measurement (typically ppm for a given isotope) that will be used along the window x axis
y: Sets the kind of measurement (typically ppm for a given isotope) that will be used along the window y axis
z1: Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window z1 axis
z2: Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window z2 axis
z3: Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window z3 axis
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 |
Create Window!: Creates a new spectrum window with the specified parameters
Selected Visible: Sets the contours of the selected spectra to be visible when the new window is made
Selected Not Visible: Sets the contours of the selected spectra to not be displayed when the new window is made
Selected Not In Toolbar: Sets the selected spectra as absent from the window toolbar, and thus not displayable at all