Main Panel¶
Clone: Clone popup window
Help: Show popup help document
Close: Close popup
Edit Spectrum Window Parameters
This popup window controls all of the settings that relate to the spectrum display windows used in Analysis. All of the spectrum windows within the project are listed and all of the details which control how they show spectra and peak lists are given, and in many cases the parameters can be edited. The settings available in this popup are often also, and sometimes more commonly, manipulated elsewhere. For example, the toggle buttons at the top of spectrum windows are usually used to control spectrum and peak list visibility. However, this popup window provides an authoritative list of all relevant settings, including a few that are not accessible from elsewhere.
The layout of the popup is divided into three tabs; the first lists the main properties of the spectrum windows and their axis, the second controls how spectra and peak lists are mapped into the windows and displayed, and the third allows the user to group windows together so that different sets may be reserved for different kinds of operation.
Windows & Axes
The first tab is divided into two sections. The upper table lists the spectrum windows which have been defined in the current CCPN project or, if the “Active windows” options is set, those in the active window group. The settings given in the table, which may all be edited, relate to general properties that govern the whole window display. Typically user may change the name of a window and adjust the aspect ratio; all spectrum window displays in Analysis preserve aspect ratio when zooming, so peaks remain the same aesthetic shape. The crosshair trace settings control whether a 1D intensity slice is superimposed upon the cursor location, although this is normally toggled on or off via the right-click mouse menu of the particular spectrum window. For both the spectrum traces that appear at the crosshair location and those that may be added to side panels (at the window’s edge) the “Slice Range” column dictates the scale that is used to show the intensity axis. In normal operation the user controls this with the <PgUp> and <PgDn> keys, rather than via this table. The last two columns of the table indicate whether strip numbers and Z axis positions are superimposed on the spectrum display (in the corners).
The lower table lists the kinds of axes are present in the selected window; the selected row in the upper table. Here the user can control whether a scrollbar to move window contents appears or not, e.g. to save some screen space. The “Panel Type” column is used to make sub-groups of window axes that otherwise have the same isotope type. The panel type definitions are set elsewhere, in the Axes popup. The panel type is only relevant for dictating where 1D ruler lines go in different windows; a ruler is only displayed on axes with the same panel type, thus the user can distinguish amide 1H axes (panel type “H1”) and other 1H axes (panel type “H2”). The last two columns adjust the depth and presence of the “Side Trace”. When visible, a side trace shows a 1D intensity graph at the edge of the window axis. Naturally, this only applies for the X & Y screen dimensions.
Spectrum & Peak List Mappings
The second tab controls how spectra and peak lists are displayed within the spectrum window selected at the top. It should be noted that spectrum contour levels and colours are set elsewhere, via the main Spectra popup. Likewise, the peak list symbols and colours are changed in the Peak Lists popup. These peaklist and spectrum settings are set on a project-wide basis, and thus are not set for an individual display window.
The upper table lists all of the spectra that may be displayed in the selected spectrum window. Here the user can control: whether a spectrum is listed in the toolbar at the top of the window, where spectra are switched on and off; whether the positive contours are drawn; whether the negative contours are drawn; and whether the 1D intensity slices, when used, include the spectrum. The last “Dim. Mapping” column is important if the user wishes to change how the data dimensions of a spectrum are mapped to the X, y & Z axes of the spectrum window, especially given that Analysis cannot always guess this correctly when there are two axis with the same isotope type. If, for example, the user has a 3D HC_cH.TOCSY spectrum and the first 1H data dimension (from the spectrum file) is displayed on the X axis, when it should really be on the Z axis, then the user clicks on the “Dim. Mapping” column. In the resulting mini-popup, changing the “Dimension 1” pulldown menu from “x” to “z1” will correct the axis mapping and effectively rotate the spectrum data as far as the window view is concerned. It should be noted that multiple windows may need to be adjusted in this way for any given spectrum; only the user can really decide what is correct, especially where data axes have been swapped.
The lower “Mapped Peak Lists” table shows all of the peak lists that may be displayed in the selected spectrum window. In the display sense, a peak list consists of a list of peak symbols (i.e. positioned crosses) and assignment annotations. The two columns of the table that can be edited dictate whether a peak list’s peak symbols and annotations are drawn, thus giving total control. However, these settings are usually controlled via the toolbar at the top of a spectrum window, and normally the peak symbols and textual annotations are both switched on or off at the same time.
Window Groups
Defining window groups is a mechanism by which different selections of spectrum windows may be made so that only some are visible at the same time. There will only be one active group of spectrum windows at a given time, and only those in this active group can be opened and will be shown in the main Analysis menu. The user can create as many named window groupings as is required and can add any window to any group. Clicking on a group in the upper table lists all of the windows in the project and whether they are included in the selected group or not. To add a window to a group, or remove it from a group, the user simply toggles the “In Group?” column. The selected group may be set as the active one by clicking on the central [Make Active] button.
Shows a table of spectrum contour windows and details of their axes
All windows: For the below table, show all of the spectrum windows in the current project, irrespective of the active group
Active windows: For the below table, show only spectrum windows that are in the currently active window group
Table 1 | |
# | Row number |
Name | Short textual name to identify the window (Editable) |
Aspect Ratio | The screen (X-Y) pixel:unit aspect ratio of the window, defaults according to isotope; “8.0” means Y axis shows 8.0 units for every 1.0 on X (Editable) |
X Crosshair Trace | Whether to show a 1D slice of the specta at the cursor position, along the horizontal screen axis (Editable) |
Y Crosshair Trace | Whether to show a 1D slice of the specta at the cursor position, along the vertical screen axis (Editable) |
Slice Intensity Range | The upper and lower intensity bounds for the 1D cursor slice display; used to scale the magnitude of the drawn amplitude (Editable) |
Strip Numbers | Whether to display strip numbers, in the upper left of each window subdivision (Editable) |
Strip Z Locations | Whether to display the Z-axis positions of each window strip, in the lower left corner of each window subdivision (Editable) |
Open: Open and display the selected spectrum window
Create New: Open a tool to create a new spectrum window; specifying names and axes etc.
Clone: Make a copy of the currently selected window, which may then be independently manipulated
Delete: Delete the currently selected spectrum window; does not affect the loaded spectra
Table 2 | |
Axis Label | A short label for identifying the axis within its window, e.g. “x”, “y”, “z1”, “z2” |
Axis Type | A name for the kind of thing represented along this axis; usually serves to subdivide frequency axes into different isotope types |
Panel Type | For a given kind of axis, which sub-type is currently set; used to differentiate axes with the same isotope (Editable) |
Scrollbar Visible | Whether the scrollbar, which shifts the spectrum view position, is displayed for the window axis (Editable) |
Side Trace Visible | For an X or Y axis, whether a 1D slice trace (at the cursor position) is displayed alongside the main contour display (Editable) |
Side Trace Height | For an X or Y axis, sets the number of pixels use for the amplitude display of 1D slice traces (using cursor position) (Editable) |
New Axis: For the currently selected spectrum window, add a new axis
Sets how spectra & peak lists are drawn in contour windows, including axis mappings; note colours are set elsewhere in peak list & spectrum tables
Spectrum Window: Selects the spectrum window to display the mappable spectra & peak lists for
Table 3 | |
Experiment | The name of the experiment record for the window-mappable spectrum |
Spectrum | The name of the window-mappable spectrum |
Spectrum In Toolbar | Whether the spectrum appears with its own toggle button in the toolbar at the top of the spectrum window (Editable) |
Pos. Contours Visible | Whether the positive contour levels are shown in the window for the spectrum (Editable) |
Neg. Contours Visible | Whether the negative contour levels are shown in the window for the spectrum (Editable) |
Slice Visible | Whether 1D slices are visible for the spectrum, if any slice displays are active for the window (Editable) |
Dim. Mapping | Sets how the spectrum dimensions map to corresponding window axes; for a given kind, enables swapping of spectrum dimensions relative to the window (Editable) |
Edit Spectra: Opens a table allowing editing of per-spectrum (rather than window) parameters
Table 4 | |
Experiment | The name of the experiment record for the window-mappable peak list |
Spectrum | The name of the window-mappable spectrum that contains the peak list |
Peak list | The serial number of the peak list, which is displayable in the spectrum window |
Symbol Drawn? | Whether the peak crosses/symbols are drawn for the peak list in the selected window; to indicate the position of extrema/resonances (Editable) |
Annotation Drawn? | Whether the peak annotation texts are drawn for the peak list in the selected window (Editable) |
Edit Peak List: Show a table of the peaks within the selected peak list
Allows spectrum windows to be grouped into sets so that only some are displayed at a given time
Table 5 | |
# | Row number |
Group | The name for the group of spectrum windows (Editable) |
Number of windows | The number of windows contained within the group |
Make Active: Sets the selected window group as the active one; only windows within this group will be displayable (in menus etc.)
New Group: Make a new grouping of spectrum windows, which can be used to quickly swap between different displayed sets
Delete Selected: Delete the selected grouping from the CCPN project; does not otherwise affect the contained windows
Table 6 | |
# | Row number |
Window | The name of the spectrum window, which may or may not be in the selected group (Editable) |
In Group? | Whether the spectrum window is part of the selected grouping; can be toggled to include & exclude (Editable) |