2D Intensity and Contour Plots
The 2D display mode is entered with commands 2D, IP or CP or from the View menu. 2D display mode is exited with command 1D or from the File menu.
A maximum of 10 positive and 10 negative contour levels can be displayed. The spacing of the levels is set with the LV command.
|Each level is set as a multiple of the minimum height (MH) parameter. The threshold can be raised or lowered by changing MH.MH can be adjusted by typing MH, or from the View/Processing Parameters menu.|
While displaying an intensity or contour plot, MH can be adjusted using the up/down arrow keys or the mouse wheel.
The color of each contour level is set with the CR command.
|Positive levels are listed on the left, negative levels on the right.Each level is set using 3 color values, for Red, Green and Blue. Each color value is between 0 and 255.|
If the user chooses to have all positive or all negative contours set to a single color, that can be set in the top portion of the dialog box. Enter the 3 color values, then check the corresponding “All” box.
For example, pure red is set with values:
255 0 0
Yellow is set as:
255 255 0
Avoid setting all values to 255, as white is invisible on a white background!
The cursor can be used to measure chemical shifts in both dimensions, to copy chemical shifts to the clipboard or to a text annotation on the screen, and to place the chemical shifts into a Data Table to build a table of assignments. See details.
The cursor can also be used to scroll through slices, overlaid on the contour plot. Press and hold the right mouse button, and move the mouse vertically across the contour plot. The slice at the position of the cursor is displayed over the contour plot. The number of the slice being displayed is shown at the bottom of the screen.
It is possible to display a high resolution 1D spectrum along any of the 4 edges of a 2D plot. The 1D spectrum must have been previously saved to a file.
The options for selecting and displaying border spectra are available from the Borders menu when in 2D display mode:
The Border scaling option (equivalent to command EP, for Edit Parameters) allows scaling factors to be entered for each border spectrum. If no border spectrum has been selected, the field in this dialog box will be blank, and any value entered into that field will be ignored.
The “clip” option truncates display at 10% of the screen height/width, and allows the scale of the border spectrum to be increased to make small peaks visible.
If the 2D plot is transposed, the top and left borders are swapped, and the right and bottom borders are swapped.
All operations involving the border spectra can be entered using the command line and in macros. Each command starts with P1, P2, P3 or P4 for the top, right, bottom and left borders, respectively. Below is a listing of all related commands, where Pn is used to represent one of these 4 commands.
Pn – If the corresponding border does not exist, this will display a dialog box allowing a spectrum file to be selected. If a border already exists, the command will toggle display of that border on/off.
Pn on – Turns on display of border n.
Pn off – Turns off display of border n.
Pn select – Displays a dialog box allowing selection of a file to be displayed along border n.
Pn select filename – Creates border n from the supplied file. filename must include the entire path, unless the file is in the current data directory.
Pn clear – Deletes border n. Note that this is not the same as turning off display of the border. This does not affect the file from which the border was created.
Pn clip – Clips, or truncates, border n.
Pn scale x – Sets the scaling factor, x, for border n.
All slices, or a specified range of slices, can be summed. If the sum command is issued with no arguments, all slices are summed. Alternatively, the command sum i j, where i and j are slice numbers, sums all slices from i to j. After execution of the sum command, the resulting 1D spectrum replaces the original 2D data as the current data. Be sure to save the 2D data before executing sum!
The sum command has the option to align, or “register”, the slices before summing. This is useful if, for example, the field had shifted during acquisition. To use this feature, in 1D display mode, use Zoom to expand the display such that the largest displayed peak should be at the same chemical shift in all slices. Exit Zoom and execute the command sum register (or sum register i j). The slices will be adjusted so that the largest peak in the zoom region is aligned, and then the slices are summed to yield a 1D spectrum.
Last updated: 2/7/08