Display of 2D contour plots
** Change as of September, 2001: **
In previous versions, 2D display was a subroutine. Commands within intensity or contour plots were single-letter commands that were executed immediately, and were not echoed on the command line at the bottom of the NUTS screen. Hitting an <ENTER> exited from the 2D display subroutine, back to the Base Level of NUTS.
In versions newer than Sept, 2001, 2D display is no longer a subroutine. It is entered by typing 2D (or IP or CP), and exited by typing 1D. With this change, commands within the 2D display mode are no longer single-letter commands.
When a 2D file is opened (with GA or from the File/Open menu), the first slice is displayed. An intensity plot (IP) or contour plot (CP) can be displayed. IP is much faster and should be used for an overview of the data, and to set frequency limits and contour levels. CP is used to view the data in detail.
In versions of NUTS newer than Sept, 2001, the command 2D is used to enter the 2D display mode, and displays an intensity plot. Exit back to 1D display by typing 1D.
Contour levels are set as multiples of the Minimum Height (MH). The levels are set in the Nuts.ini file, but can be changed after starting Nuts using the LV (levels) command. The minimum height is expressed as a percentage of the tallest peak in the entire data set. So, the first step is to find the intensity of the largest peak and from that to set the display scale. This is done with SS (or Set Scale from the 2D menu).
Contour level colors are set in the nuts.ini file or can be set from within NUTS using the CR command.
By default, the first contour level is at the minimum height, which the user can change by typing MH. The choice of this setting depends on the type of data being displayed. For HETCOR data, where all peaks are approximately the same intensity, a value of 10% is reasonable. For NOESY data, in which the crosspeaks are much smaller than the diagonal, the MH value can be as small as 0.1%.
Starting with December 2001, the MH value can be changed while the intensity or contour plot is displayed. This is done using a scroll bar displayed on the right edge of the screen, or with the PageUp, PageDown, Arrow Up, Arrow Down, "<" key and ">" keys. Due to the speed of contour plot recalculation, especially on older PCs or with large 2D data sets, this is best done in the intensity display mode or in a zoomed region if in the contour display mode.
Text labels for the axes can be entered from the View/Spectral Parameters menu in the NUTS base level (not in the 2D display routine).
Display an intensity plot with the 2D or IP command (or from the 2D menu). Intensity plots are much faster than contour plots, so it makes sense to use that display mode for an initial look at the data. The size of the plot is adjusted by choosing Edit Display Parameters from the Edit menu, and entering a value for the margin on each side.
The chemical shifts in both dimensions can be displayed by pressing and holding the left mouse button.
The Zoom expansion routine can be used to display chosen regions. Type ZO to enter the Zoom routine, then press and hold the left mouse button and drag across the region of interest. Type Ctrl-E to expand to the chosen limits, or click the right mouse button.
Change to contour plot, instead of intensity plot, by typing CP (for versions of NUTS older than Sept, 2001, this is done with the single-letter command C). Note the other options available from this menu.
Slices can be displayed overlaid on the contour plot. Press and hold the left mouse button, place the cursor on a peak of interest and then press and hold the right mouse button also.
(Users with a single button mouse should press the period key on the keyboard instead of the right mouse button.)
Projections can be displayed along each axis from the Borders menu or using the commands P1, P2, P3 and P4 which toggle on/off display of projections along the top, right, bottom and/or left edges, respectively. (In versions of NUTS older than Sept, 2001, this is done with the single-character commands 1, 2, 3 and 4.) The vertical scale for each projection is set independently by choosing Edit Display Parameters from the Edit menu, and entering a multiplying factor for the chosen projection. If the projection contains both large and small peaks, it is possible to scale up the projection to see the small peaks, and then clip (truncate) the taller peaks. Clipping is turned on and off from the Display menu.
If high resolution 1D spectra exist, they can be displayed instead of the actual projection by selecting Pick the Bottom/Top/Left/Right Spectrum from the Borders menu. If such spectra have been defined, their display is automatically toggled on. As with the calculated projections, the vertical scale of high resolution "projection" can be adjusted by choosing Edit Display Parameters from the Edit menu. Either projection can be clipped, allowing small peaks to be seen while limiting the height of larger peaks. This is available from the Display menu.
The 2D plot can be resized by typing EP or selecting Edit Display Parameters from the Edit menu. The Margin for each side is set independently, entered as fraction of total display.
Last updated 3/6/06