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Spectrum Window Contour Display

The spectrum display in Analysis displays NMR spectra of arbitrary dimensionality and allows the user to identify signal peaks and assign them to atomic resonances. A CCPN project may contain as many spectrum windows as memory allows with whichever axis types the user requires.

Simple 1-dimensional spectra are displayed as intensity graphs, but higher dimensionality spectra are displayed as contour plots. A contour plot represents the intensities in the plane of an NMR spectrum and each contour line represents points of equal data value (height). For a 2-dimensional spectrum there is only one displayable spectrum plane, but for 3D and higher there are many planes, which can be imagined as being stacked on top of one another along depth axes. The user can navigate to view any position in a spectrum by changing the region of the plane displayed in the screen and independently adjust what the current depth position is. Also, in windows with depth axes Analysis has the ability to display several planes at once in a specified depth region, i.e. a given thickness. A spectrum window always has the same kind of spectrum dimensions (e.g. in terms of isotope) represented by the on-screen (X,Y) and depth (Z) axes. If an alternative, orthogonal view is required, for example to show different NMR axes in the plane of the screen then a new window must be made. However, if the user simply wishes to swap spectrum data axes that have the same kind of isotope then this can be done without having to make a new window; the mapping of spectra into windows can be adjusted via the “Spectrum & Peak List Mappings” section of the main Windows option.

There are three basic components to a spectrum window popup: there is the main graphical spectrum display with axes and scrollbars, which may be sub-divided into several strips/panels; a toolbar of buttons at the top, which control what is displayed in the window; and also a menu accessible with a right mouse click over the main display, which has a large amount of important functionality.

Top Toolbar

The toolbar of buttons above the main spectrum display area allows the user to control various aspects of what is displayed. After clicking on one of the top buttons an extra panel will appear to give access to further options, and clicking on the same top button again will make the options panel disappear.

Spectra

The [Spectra] option allows the user to toggle individual spectra within the main display on or off. The spectra that can be displayed are naturally those that have the right kinds of isotopes on their axes for the spectrum window. Although, a spectrum may be displayed at least the X & Y axes match, i.e. a 2D spectrum can be displayed in the X-Y plane of a 3D window. Spectra may be prevented from appearing within this toolbar, to avoid overcrowding, by changing the “Spectrum In Toolbar” column within the “Spectrum & Peak List Mappings” section of the main Windows option.

Spectra may also be toggled on an off using keyboard shortcuts, which are set in the main Spectra display options. Also, the order in which spectra are drawn is reflected in the order that they appear in the top panel; this is set via the “Rank” of the Spectra display options.

Contours

The [Contours] option allows the user to adjust the contour base level (green arrows), the number of contour lines and flip between positive and negative levels. These settings will be applied to all of the visible spectra in the window. Hence, it is common for the user to toggle certain spectra off first if they should not be affected. These contour settings are fairly simple, but more detailed control of contours is given by the [More..] button which opens the main Spectrum Contour Levels popup.

Peaks

The [Peaks] option allows the user to control which peak lists, in terms of the peak markers and annotations, will be visible in the main graphical display. The user simply clicks on the button of a peak list to turn it on or off. By default the “Multi-list” option is set so that any number of peak list will be displayed, otherwise the user can uncheck this so that only one peak list is shown at a time. Having only one peak list shown is useful to avoid picking peaks in the wrong spectra; peaks will only be picked in displayed peak lists.

It should be noted that when a spectrum has more than one peak list only one of these will be active; the active peak list is the one that the user can select in the spectrum and the one newly picked signal maxima are placed in. To change the active peak list for a spectrum and how peak lists are shown (symbol type and colour) the user should edit the main Peak Lists table.

Strips

The [Strips] option controls how the graphical spectrum display is sub-divided. These sub-divisions are called “strips” and allow the user to have different panels in the window showing different regions on the spectra. All strips will be tied together along one axis; with vertical strips the Y-axis is the same for all sub-divisions, and for horizontal strips the X-axis is common. Strips can be added and removed by the user, although many systems in Analysis will automatically curate strips (e.g, for protein sequence assignment). The strips’ panel also indicates which strip in the window is deemed to be active (its button will be green); it is the active strip that can be moved with the green arrow and is the target of any navigation options into the window.

Spectrum windows in Analysis have another way of defining sub-divisions which are called “separators”. These are distinct from strips and are not generally administered from the toolbar (except the ability to remove them all). A separator is a sub-division that goes at right angles to the main strip divisions and serves to split the axis which is not affected by the strips. For example a window with vertical strips can have horizontal separators which split the Y-axis into separate regions to display separate PPM ranges (e.g. CA, CB, C’). Separators may be added via the right mouse Window Menu.

Coordinate Location

The last button in the top toolbar displays the current location of the mouse cursor for the window. Clicking on the button opens the Center coordinates panel which allows the user to specify a particular location for the center of the window view and also allows the cursor location to be displayed in Hz units, rather than PPM.

Spectrum Display Area

The main graphical display area is where spectrum lines, contours and peak markers are displayed. At the edge of the area are tick axes with numbers indicating the display region (usually in PPM). The display region may be changed by using the scrollbars or the various mouse controls listed below. Note that the scrollbars may be removed to save space using the right mouse Window Menu. The box at the bottom right corner where the tick axes meet shows the position of the current view, according to zoom level and position, relative to the maximum possible extent of the window axes.

For 3D and higher dimensionality windows there will be extra scrollbars at the bottom representing the depth axes. The current position of these is displayed to the left of the scrollbar, and this may be set by typing in the entry box. These depth (or “orthogonal”) scrollbars are different to the X-Y scrollbars because they also control the thickness of the depth view (i.e. the number of planes deep to show contours for). To change the thickness of a view the left or right edge of the depth slider can be expanded or shrunk using the middle mouse button.

Window Navigation

The cursor may change the region of the spectrum (or spectra) displayed in the graphical area by using both keyboard and mouse controls that allow the view to pan, zoom and change orthogonal depth position. These controls are summarised as follows, noting that the middle mouse button is specialised for these functions:

Pan Window:Arrow keys Middle-click + drag
Zoom In/Out:<PageDown>/<PageDown> Scroll wheel forward/back <Shift> + Middle-click + drag up/down
Zoom To Region:<Control> + Middle-click + drag region
Depth Scroll:<Control> + scroll wheel forward/back <Shift> + scroll wheel forward/back

Peak Picking

The intensity maxima and minima in NMR spectra which represent the locations of resonance signals may be marked as being a peak, i.e. “picked”. Picked peaks are marked with crosses at their centre and carry an assignment annotation to indicate the resonances from which the peak derives. For an unassigned peak this annotation will just be dashes (one for each spectrum dimension).

Spectrum peaks may be picked in three basic ways in Analysis: by specifying an exact peak location with the mouse, by dragging a rectangular peak-find region with the mouse to find extrema, and by using the “Region Peak Find” functionality of the Peak Finding section to find extrema in a large spectrum region. In all cases newly picked peaks are placed in the active peak list for a given spectrum (set in the Peak Lists popup). The mouse and keyboard controls used to pick peaks are listed below, noting that the <Control> key and left mouse button are specialised for this purpose:

Pick Peak at Mouse Position:
 <Control> + left-click
Peak Peaks in Region:
 <Control> + <shift> + left-click & drag

It should be noted that when peaks are picked all visible spectra are considered for picking, but only if their active peak list is toggled on (via the top tab). By default, if an exact peak position is specified then new peaks will be picked in all visible spectra. Similarly, when dragging a box to find intensity minima/maxima in a region, peaks are picked for the extrema found in all visible spectra. If the user wants to avoid picking peaks in specific spectra then a spectrum can be toggled off in the top panel, or the active peak list for the spectrum can be toggled off (leaving any contours visible). For the region search peaks will be located according to the “Find Parameters” set in the Peak Finding popup; by default extrema are only found above the same threshold that contours are displayed for.

Note that if a spectrum is tiled so that its contours are visible outside the normal bounds any peak picked in a tiled region will be picked at the apparent PPM value; the peak is recorded internally at the equivalent position inside the spectrum, but its position is automatically “unaliased” to move it outside the spectrum width. Here the underlying, aliased peak inside the spectrum width will also be displayed, albeit with a dashed cross.

Peak Selection

Specific visible peaks may be selected to that specific operations may be performed on them (assign, delete...). Peaks that have been selected are displayed with a solid box around their marker crosses. Peaks can be selected in several different spectra and in several different windows, even if the peak locations are not currently visible; so caution should be used when deleting peaks. Beak selections can be defined and added to according to the mouse controls listed below, noting common use of the left mouse button. Also, a number of operations may be performed on the selected peak(s) by using keyboard shortcuts.

Select Single Peak:
 Left-click at center
Select Several Peaks:
 Left-click & drag box over peaks
Add Single Peak To Selection:
 <Shift> + Left-click
Add Several Peaks To Selection:
 <Shift> + Left-click & drag box over peaks
Clear Peak Selection:
 Left-click in a region without peaks
Move Selected Peak:
 <p> + drag mouse
Re-center Selected Peaks:
 <P>
Assign Peak Under Mouse:
 <a> (opens Assignment Panel)
Show Selected Peaks Table:
 <s> (opens Selected Peaks)
Delete Selected Peaks:
 <Delete>
Move Selected Peaks Label:
 <q> + drag mouse

Note that the keyboard shortcuts listed are the default settings and could actually be different. All keyboard shortcuts are listed (and can be changed) in the “Macros” section of the User Options popup.

Marker Lines & Rulers

The user may place dashed, multi-dimensional marker lines (i.e. a big cross) at the current mouse location using <m>. Also a 1-dimensional dashed ruler line may be placed at the mouse location using <h> for a horizontal line and <v> for a vertical line. Any multi-dimensional mark that is suitably close to a peak will automatically lock on to the exact peak location. The <n> key is used to remove all marks and rulers.

For a detailed description of marker lines and rulers and their various options see the Marks and Rulers documentation.

1D Traces

An spectrum window can additionally carry a number of 1-dimensional (i.e. intensity graph) slice traces, which show a cross section through the displayed spectra at the current mouse location. Such slice traces may be added via the right mouse menu “Window” option, selection either crosshair traces that are superimposed in the main graphical display or side traces that are shown as extra panels to the side of the window.

Right Mouse Menu

The right mouse button, when pressed over the graphical display area, will open up a menu that allow the user to perform various operations. These functions are sub-divided into the main categories listed below. For more detailed descriptions see the Window Menu section.

Assign

These options control the assignment of the selected peak or peaks to resonances and spin systems (intra residue groups). For example the user can assign a peak, propagate (spread) assignments over several peaks, remove assignments etc.

Peak

These options relate to general operations performed on peaks, including deletion, setting aliasing, setting details and arranging labels. Many of these functions have keyboard shortcuts (see “Macros” section of the User Options).

Locate Peaks

These functions are used to find the selected peaks in the spectrum window or use the locations of peaks to navigate to matching peaks (or equivalent positions). Some of these options include navigation to other windows.

View

The view functions control the current spectrum region being displayed and the contour levels.

Navigate

The navigation options allow the user to locate equivalent positions in other spectrum windows based upon the mouse location. Such locations are found in windows that have at least some of the same kinds of axes as the current window. For example the user may navigate from a 2D HN window displaying an HSQC spectrum to the equivalent HN (amide) position in a 3D window.

Strip

These options are used to control strips and separators; the two kinds of spectrum window sub-division.

Markers

The marker options control the presence of dashed position marker lines; both multi-dimensional markers and 1-dimensional rulers.

Window

This section provides various general functions for the spectrum window which include: making a duplicate “clone” of a window, printing a window to file (e.g. PDF) and controlling the 1D slice traces.

Macros

This menu contains lists any Python macro scripts that have been added to Analysis (see User Options) to operate in the context of a spectrum window.

Main Panel

button Spectra: Opens a panel toggle the display of individual spectra on or off

button Contours: Opens a panel to change contour levels for the currently displayed spectra

button Peaks: Opens a panel toggle the display of individual peak lists (cross marks and annotations) on or off

button Strips: Opens a panel to control the number, order and orientation of strips (parallel window sub-divisions)

button 8.663, 104.16 (1H,15N): The current cursor location for the window axes, click to center the view or change cursor position units

button Help: Show popup help document

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