Spectrum Attributes

This dialog collects together a wide variety of controls for interacting with spectral display windows. Only one window is controlled at a time through this dialog.

The Attributes Dialog is composed of an icon bar across the top and a tabbed window which forms the majority of the dialog. The Icon Bar has a subset of icons and functions of the icon bar that appears at the top of all standard spectrum windows. above. The tabbed window allows the user to select from a series of panel controlling different aspects of the interface. The various tapped panes that compose the Attributes Dialog are described in the following sections.

Data Selector Panel

Data Selector

The dataset selector panel is used to control which datasets are displayed in the currently active spectrum chart. The left panel lists all datasets that are available to be added to the chart. The right panel lists all datasets currently selected for display in the chart. Use the buttons between the two lists to add or remove datasets from the selected display list. The order that datasets are added to the display list determines the order in which they are drawn (there is not yet, but will be, a method to rearrange the list). You can mix datasets of different dimensionality, but higher dimensional datasets should be listed above lower dimensional datasets. Click the Refresh button after changing the display list to update the actual spectrum display.

Dataset Panel

Datasets

The Dataset Panel is used to control the colors and levels used to render the spectra. Multiple datasets can be assigned to a single spectrum chart. Each dataset is represented by a row in the Dataset Table in this panel.Most columns of the header have a menu that appears when you right click on the header. This provides controls that can be used to set the parameter for that column across the whole list of tables. Most columns have at least a unify entry in the menu. By setting the first rows entry to a certain value, and then choosing unify you will set all rows to that value. This always applies the value in the first row to the remaining rows. Menu entries that are specific to individual columns will be described below.

By default, the rows displayed in the table correspond to the datasets that are displayed in a single, active spectrum chart. Choosing the Scene setting above the table displays all the datasets in the entired window (technically, the JavaFX Scene, hence the name). This is useful if you want to change values for all the datasets in the window.

At the bottom of the table is an attribute selector and slider. Use the selector to choose an attribute (lvl, offset, nlvl, and clm). You can then adjust the slider to change the value of that parameter. As you move the slider the value in the table and the spectrum in the associated chart will update. If any of the rows in the dataset table are selected the parameter value for those selected datasets will be adjusted. If no datasets are selected then the value for all datasets will be updated.

The columns in the table are as follows:

dataset

This column contains the name of the dataset whose properties are displayed and controlled by that row of the table.

lvl

This column contains the contour threshold (for 2D displays) or vertical scale (for 1D displays). It is adjusted by using the Auto, Higher and Lower toobar buttons. You can also click on the value to activate it for editing and then type in new value. Hit the Return key to complete editing the value and hit the Refresh button to redraw the value. The level column header has a pop-up menu (right click). Choose "unify" to set the level for all the datasets in the table to the level value of the first dataset.

Positive & Negative

The Positive and Negative column groups each contain three columns: on, color and width. Those under positive, control the display of 1D lines, and positive contours in 2D plots. Those under negative control the display of negative contours in 2D plots

On

The on column contains a checkbox and must be turned on (the default) for 1D lines or 2D contours to be displayed. The pop-up menu for the on column has two items, all on and all off. These can be used to control the display status of all the datasets of the table.

Color

This column controls the color used for contours and 1D lines (the positive column only). Click on the colored rectangle to display a Color Selection Dialog. You can choose a color from the palette that appears, or select *Custom Color... to get a second dialog that allows selecting a color based on HSB (Hue, Saturation, Brightness) or RGB (Red, Green, Blue) values, or entering a web style color descriptor (like #ff0000).

After you choose a color in the color dialog, you'll see the colored rectangle change to reflect the new color but you need to click the "Refresh" button to actually refresh the spectrum with the new color.

The color column menu has three entries: unify, interpolate and schema. Unify works as described above. Interpolate will set each row to a color that is interpolated between the colors of the first and last rows. Schema will display a dialog in which you can select from a variety of predefined color schema. Interpolate and schema would typically be used for sequential coloring of spectra used in ligand titrations.

Width

This specifies the width of 1D and contour lines. The width column has a pop-up menu with a unify choice, which can be used to set the width of all datasets to that of the first dataset.

Color Schema

The color schema dialog allows the user to select multiple colors that will be applied to the datasets currently listed in the dataset table. A schema can be applied to the spectra by clicking the button with the schema name. The colors used in the schema are those used by the Vega visualization software.

Multiple schema are available and they are grouped in to related sets. The categorical schema consit of a set of a specific number of discrete colors. If the number of datasets to be colored is smaller than the number of colors, then only the required number of colors are used. If more datasets are to be colored than the number of available colors then, in the current implementation, the available colors are wrapped so that the colors are reused.

The sequential and diverging schemes are used when one wants an approximately continuous range of colors. These are useful when the datasets differ by some quantitative value such as ligand concentration. The snglseq schema consist of a range of colors chosen from a single hue, whereas the multiseq and multiseq2 schemas consist of colors of that use multiple hues. The diverging schema are appropriate where there is some midpoint dataset and colors should diverge away from the color at the midpoint. They are generally less useful for NMR titration experiments. If the number of datasets to be colored is different than the number of colors available in a sequential or diverging dataset then interpolation will be done to create the specified number of colors.

The reverse checkbox can be used to reverse the order of the colors in the schema so that the first dataset gets the last color and the last dataset gets the first color in the schema. Changing this setting will update the color display, but you have to reselect a schema (click the button to the left of the scheme) to apply it to the spectra.

Sometimes the colors at the edge of the spectra may be too light or dark. You can use the range slider at top of the schema window to limit the range of colors that are used. This is only used for the squential and diverging schema. As with the reverse button, changing the values will immediately update the schema display, but you need to select a schema to apply the updated colors to the spectra.

Schema

View Panel

View The View panel is used to select plot regions, control which dimension of the dataset is displayed on which axis of the plot, and control the display of integrals and regions. Note that some of these values can be changed more quickly via the toolbar at the bottom of each spectrum window.

X

Press the Left Mouse button over the X to pop-up a menu of predefined plot limits, or enter values in the next two text fields to set the plot limits (in ppm) for the x (horizontal) axis. If the entry is followed (without an intervening space) by a "p", then the value is considered to be in units of points of the dataset. The minimum and maximum plot limits can be entered in either order. These values are automatically set to give the full spectrum when a new dataset is assigned to this window.

The text in the third field is used as a label for the x (horizontal) axis. This value is used to label the axis on hard copy plots, is used for determining the correlation of cursors between different windows (see cursors, below), and is used during peak-picking and peak display (see Peak Picking, below). This is automatically set to the value assigned to the corresponding dimension (see below) during the referencing of the matrix, but can be changed by entering a new value in this field. 1(2,3,4) Hold down MENU over this item to select the dimension of the matrix to be displayed on x axis.

Y

Press the Left Mouse button over the Y to pop-up a menu of predefined plot limits, or enter values in the next two text fields to set the plot limits (in ppm) for the y (horizontal) axis. If the entry is followed (without an intervening space) by a "p", then the value is considered to be in units of points of the dataset. The minimum and maximum plot limits can be entered in either order. These values are automatically set to give the full spectrum when a new dataset is assigned to this window. The text in the third field is used as a label for the y (vertical) axis. This value is used to label the axis on hard copy plots, is used for determining the correlation of cursors between different windows (see cursors, below), and is used during peak-picking and peak display (see Peak Picking, below). This is automatically set to the value assigned to the corresponding dimension (see below) during the referencing of the matrix. 1(2,3,4) Hold down MENU over this item to select the dimension of the matrix to be displayed on y axis.

Z

Press the Left Mouse button over the Z to pop-up a menu of predefined plot limits, or enter values in the next two text fields to set the plot limits (in ppm) for the z (3rd Dimension) axis. If the entry is followed (without an intervening space) by a "p", then the value is considered to be in units of points of the dataset. The minimum and maximum plot limits can be entered in either order. These values are automatically set to display the full range of planes when a new dataset is assigned to this window. If the return key is pressed in the first Z field, then the second field will be set to the same value. The popup menu has a convenient entry to select the first or last plane. The spectral display window will be cleared prior to drawing the first plane is set. Subsequent planes will be overlaid on top of the first plane. To draw a single plane, set both values equal to each other.

Z2

Press the Left Mouse button over the Z2 to pop-up a menu of predefined plot limits, or enter values in the next two text fields to set the plot limits (in ppm) for the z2 (4th Dimension) axis. If the entry is followed (without an intervening space) by a "p", then the value is considered to be in units of points of the dataset. The minimum and maximum plot limits can be entered in either order. These values are automatically set to display the full range of planes when a new dataset is assigned to this window. If the return key is pressed in the first Z2 field, then the second field will be set to the same value. The popup menu has a convenient entry to select the first or last plane. The spectral display window will be cleared prior to drawing the first plane is set. Subsequent planes will be overlaid on top of the first plane. To draw a single plane, set both values equal to each other.

Integrals and Regions

The Integrals and Regions section of the View tab can be used to turn on and off the display of integrals and regions and control aspects of their display. The following figure shows a spectrum with both displayed. Additionally, one integral has been selected, allowing its position to be adjusted.

Integrals and Regions

Integrals

Integral lines can be drawn on one-dimensional spectra. Turn their display on or off with the Integrals check box. The position of the integrals display line is always a certain fraction of the vertical display region and the start and stop of this can be controlled with the range slider. The largest integral in the spectrum will occupy the full fractional range. Other integral regions will be scaled proportionally to magnitude of the integral.

Regions

Regions (used for integration etc.) in one-dimensional spectra can also be displayed. Use the Regions check box to turn their display on or off. The regions will be displayed as a filled yellow box spanning the full y-range and the x-range between the start and stop of the region.

Style Panel

Style

The Style panel is used to control various colors, font sizes, borders and the display of a grid and dataset titles.

Colors

The colors section allows you to control the color of the background, axes, and crosshairs. Each attribute has a color chooser and a checkbox. If the checkbox is turned off that attribute will use a color set in the main NMRFx preferences dialog. If it is turned on, you can set the color for this specfic spectrum with the color chooser.

Fonts

The font size for tic marks and axis labels can be selected with these two choosers. When you change the font size the border will be increased to a large enough value that the tic mark labels and axis labels are fully visible.

Borders

These controls set a minimum border size for the top,bottom left and right borders (based on the position of the control). Note: the border size may be bigger than that seledcted if a larger size is necessary based on the selected font sizes (see above).

Grid

If this checkbox is selected, then grid lines will be drawn. Grid lines are drawn at the position of the major tic marks (the ones with numerical labels).

Titles

If this checkbox is selected, then each dataset displayed in the spedctrum chart will have a title. For 2D (or higher) displays the labels will appear starting at top left of the spectrum. If more than one dataset is present they will be arranged to the right of previous label. If the top border is large enough the titles will appear in the border area, otherwise they will appear just under the top border line (inside plot area). For one-dimensional spectra the title will just above the spectrum baseline at the left edge of plot. If multiple 1D datasets are present the vertical location depends on whether there is a vertical offset between each dataset. If there isn't, or it's too small, then a calculated vertical displacement will be used to offset the labels so they don't overlap. If there is sufficient offset between spectra, then the title will be drawn just above each spectrums baseline.

Slices Panel

Slices

Slices (1D vectors extracted from dataset) can be drawn in a horizontal and vertical orientation across the spectrum. Slices are turned on with the checkbox in the control region below the spectrum, and their appearance is controlled with this dialog. Two slices can be drawn, one at the position of the black crosshairs and one at the position of the red crosshairs. By default, only the first is drawn.

Offset Tracking

By default the slices are drawn with an offset to position them at the center of the spectrum. This offset value can be changed with the Vertical and Horizontal Sliders. If the Offset Tracking checkbox is selected then the slices will be automatically positioned to be drawn so they are centered at the current postion of the crosshairs.

Colors

: By default, the slices are drawn with the color of the dataset they are slicing. If you turn off the Use Dataset Color checkbox then the color of the slices will be controlled by the two (one for each pair of slices) color slectors.

Slice

The checkboxes under On is used to turn on / off the display of each pair (vertical/horizontal) of slices. By default only the first (corresponding to the black crosshair position) is drawn.

Scale

Type an entry in this box to specify the scale value at which 1D slices are to be drawn. This value is multiplied by a global scale parameter (set in the Prefs dialog, default 1e6) to generate the actual value that is used. The up and down arrows provide a convenient means to increment or decrement the scale level. Clicking on the up arrow raises the scale level to a value equal to the current level times the current value of the multiplier (the value in the next field). Clicking on the down arrow lowers the scale level to a value equal to the current level divided by the current value of the multiplier (the value in the next field). Whenever the Levelvalue is changed the Scale value is changed to be 10.0 times the Level value as this generally provides good results.

Offset for Vertical Slices

Select a value using the slider to specify the offset position(from 0.0 to 1.0) at which X (and Z) slices are drawn. be drawn. Only active if Offset Tracking is off.

Offset for Horizontal Slices

Select a value using the slider to specify the offset position(from 0.0 to 1.0) at which Y (and Z2) slices are drawn. be drawn. Only active if Offset Tracking is off.

Peak Selector Panel

Peak Selector

The peak selector panel is used to control which peak lists are displayed in the currently active spectrum chart. The left panel lists all peak lists that are available to be added to the chart. The right panel lists all peak lists currently selected for display in the chart. Use the buttons between the two lists to add or remove peak lists from the selected display list. The order that peak lists are added to the display list determines the order in which they are drawn (there is not yet, but will be, a method to rearrange the list).
Click the Refresh button after changing the display list to update the actual spectrum display.

At the bottom of the Peak Selector tab is a choice box which allows you to select what peak lists are available to be displayed. The three choices are, Matching, Compatible and All. When set to Matching, only peak lists that have the same dimension label values (like HN, 13C, CA, N etc.) as the dataset dimensions are listed. When set to Compatible, peak lists only need to have matching nuclei typesd (13C, 15N 1H etcv.) in order to be listed. This allows you to select and display peak lists that don't have exactly matching names. All lists are shown when set to All.

Peak Panel

Peaks

The Peaks Panel is used to control the colors and other options used to render the peak lists. Multiple peak lists can be assigned to a single spectrum chart. Each peak list is represented by a row in the Peak List Table in this panel.

The columns in the table are as follows:

on

The on column contains a checkbox and must be turned on (the default) for this peak list to be actually displayed.

oncolor

The color of the peak annotation can be one of two values. The choice of value is dependent on a property of the each individiual peak and this property is selected in the ColorType column. The "on" color, chosen in this column, is the color used when the selected property is in the true state. Click on the colored rectangle to display a Color Selection Dialog. You can choose a color from the palette that appears, or select *Custom Color... to get a second dialog that allows selecting a color based on HSB (Hue, Saturation, Brightness) or RGB (Red, Green, Blue) values, or entering a web style color descriptor (like #ff0000).

After you choose a color in the color dialog, you'll see the colored rectangle change to reflect the new color but you need to click the "Refresh" button to actually refresh the spectrum with the new peak list color.

offcolor

The color of the peak when the selected peak property is in the "off" state.

colorby

The property used to determine the peak coloration. There are five choices and these are described in the section below.

type

The display type used for drawing the peak indicator. The types are described below.

npl

Only used for 3D (or higher) dimensional datasets. If a single plane is drawn and this value is set to 0, only peaks that are closest to the displayed plane will be drawn. If set to a value greater than 0, then peaks that are no more than that many planes above, or below, the displayed plane will also be drawn. For example, if set to 1, you'll see peaks that are exactly on the displayed plane, and peaks that are one plane above and one plane below the displayed plane. You can distinguish, by color, peaks exactly on the display plane from those off the plane by having the colortype field set to Plane

lnk

Peaks can be linked to other peaks in one or more dimensions. If this field is set to true then lines will be drawn between the linked peaks.

sim

Only used for 1D datasets. If turned on, each peak will be displayed with one or more Lorentzian lineshapes. Multiple components are drawn if a Multiple Analysis has been done and the peak is a doublet or higher.

label

Each displayed peak has a label drawn next to it. By default (Peak setting) this label is an integer number representint the peaks unique peak identifier.

Peak Color Types

The ColorType field listed above controls how the color of peaks are determined. The following are the different modes that can be used.

Plane

Used for 3D (and higher dimension data). True (on) if a single plane is drawn and the peak is exactly on it. False (off) if the peak is not one or more planes away from the displayed plane. This option is only appropriate if the npl setting is set to one or more.

Assigned

True (on) if the peak is assigned. False (off) if it is not assigned. To be assigned it needs to have a non-empty label for each dimension.

Error

Peaks can have an error field that depends on whether there are adjacent peaks found when picking. If any dimension is not set to "++" the state will be False.

Status

Peaks have a status value. Peaks originally have the status value set to 0. If the status value has been changed to a value greater than 0 the peaks property will be false (off) for purpose of the color choice.

Intensity

If the peak intensity is positive the peak will have the true (on) state. if the peak intensity is negative it will be false (off).

Peak Display Types

By default, peak positions are displayed with a box, but the Type field listed above, allows you to choose from six different modes.

Peak

The peak position is annotated with a box centered on the peak position, with a width equal to the peak bounds. A label is placed at the corner.

Cross

The peak is drawn as a cross centered on the peak position, with a width equal to the calculated ellipse size (see below). A label is placed at the corner.

Label

The peak position is labeled, but a box is not drawn. A line is drawn from the label position to the peak center.

Ellipse

The peak position is drawn with an ellipse centered on the peak position. The width of the ellipse is calculated based on the linewidth. The area inside the ellipse is that used for elliptical volume integration and is a size chosen to optimize the signal to noise ratio of the calculated integral.

FillEllipse

Same as Ellipse (see above), but the ellipse is filled. Useful for drawing simulated peak lists.

None

The peak position is labeled, but a box (or other annotation) is not drawn. Unlike, Label mode, no line is drawn from the label to the peak center.

Peak Label Types

The label that is displayed next to each peak annotation is controlled by the Type field. The following are the choices that can be used.

Number

The label is the peak number.

Label

The label is composed of the assignment labels for each peak dimension.

Residue

The label is composed of the unique residue numbers from the assignment label for each peak dimension.

SglResidue

The label is composed of the unique residue number preceded by the single letter residue type. Only applicable if the peak dimension labels include this.

Atom

The label is composed of the atom fields from the assignment label for each peak dimension.

Cluster

The label is composed of the number of the cluster (as used in RunAbout) for each peak dimension.

User

The label is composed of the user field for for each peak dimension.

Summary

The label is composed of a summary of information about the peak based on shift and multiplicdity. Only relevant for 1D peak lists.

PPM

The label is composed of the chemical shift of the first dimension. Normally used for 1D peak lists.