The amount of information in an NMR spectrum is generally so great that it is often only informative to look at a portion of the spectrum at one time. In NMRViewJ, sub-regions may be selected by limiting the region limits on the x or y axis of the display, and/or choosing a sub-selection of planes in spectra with three or more dimensions.
The View Panel provides controls to interactively select the display regions. It is itself divided into three subregions. The first contains a series of "combo boxes" for selecting display modes, the second contains a group of controls for selection region limits and dimensions, and and the third provides an interactive graphical view of the display region.
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- Dimensions
This menu provides control of whether the spectral display is a one dimensional vector drawing, or a two dimensional contour plot.
- 1Dx
In this mode the the spectrum is displayed as one or more one-dimensional vectors in a horizontal orientation.
- 1Dy
In this mode the the spectrum is displayed as one or more one-dimensional vectors in a vertical orientation.
- 2D
In this mode the the spectrum is displayed as a two-dimensional plot.
- Mode
The selected entry in this menu determines whether or not contour data is read from the matrix or a contour file..
- Live
Data for the contour plot is obtained from the matrix file.
- Record
Data for the contour plot is obtained from the matrix file, but the contours are recorded in a file for future playback. Only those planes that are actually drawn while in this mode are recorded.
- Play
Data for the contour plot is obtained from the contour file that was created in record mode.
- 1D Offsets.
This determines how the ofsets between 1D vectors are calculated when more than one spectrum (or row) is drawn in a single window.
- 0
With a setting of 0, there will be no DC ofset between spectra.
- 1
With a setting of 1, the DC offset will be calculated so that spectra will be evenly spaced across the vertical range of the spectrum.
- 2
With a setting of 2, the DC offset will be taken from the "deltaoffset" parameter, set with "nv_win deltaoffset".
- 3
With a setting of 3, the DC offset will be calculated so that the spectra will be evenly spaced across the vertical range of the spectrum.
- 4
With a setting of 4, the DC offset will be caculated from the "deltaoffset" parameter and the number of spectra to be displayed.
- DCOffset1D.
This only effects the display of vectors (either true 1D spectra, or slices of higher dimensional spectra). If selected then the spectrum will be offset so that the edges of the spectrum will be displayed at zero. This is accomplished by subtracting a straight line calculated between the left and right edges. The offset is dynamically calculated as the spectrum plot limits are changed. The effect is only really appropriate when the spectrum is positioned so that the left and right eddges are "baseline" regions.
- 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 (if AUTOCLEAR) 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 (if AUTOCLEAR) 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.
The zoombox in the lower right corner of the spectrum provides a graphical view of the current display region. The display region can also be changed by interactively dragging the zoombox around. The current display region is shown as the blue box. The position of the view can be adjusted by pointing the cursor near the middle of the box, holding the left mouse button down, and dragging the blue view box around. The size of the view region can be adjusted by pointing the cursor near an edge of the box, holding the middle mouse button down, and dragging the side to its desired position.
The two rectangular regions at the right side of the zoom box display the current display ranges for the 3rd and 4th dimensions of the datasets (with these higher dimensions). A horizontal blue line will be drawn at the relative position of the selected display planes. The width of the line will represent the number of selected planes. You can use the mouse to drag the blue line to a new position, or change its width, and thereby update in real-time the display planes for the current spectra.