Strip Plots

Strip plots are a very useful means of presenting sequential assignment data. The integration of the Tk toolkit into NMRView allows the user to create almost any sort of display, including strip plots. A convenient way to create strip plots, however, is by using the Strip Plot GUI illustrated below (You can click on the image to get an expanded view). As with all of the NMRView tools, the Tcl source for the Strip Plot GUI can be used as a starting point for more complex interfaces. The use of the existing GUI is summarized below.

The Strip Plot GUI automatically generate strip plots based on the positions of a series of specified peaks. Several means are provided for specifiying the peaks, and the order of the peaks can be conveniently reordered. The list box on the right side of the Strip Plot GUI contains the peakSpecifiers used to generate the plot limits for each window that composes the strip plot. One spectral window in the plot will be created for each peak in the list. There is, however, a maximum number of windows that can be displayed in the Strip Plot. If the number of peaks exceeds the maximum number of windows the scrollbar at the bottom of the Strip Plot can be used to adjust the range of peaks that are displayed. The X axis limits for each spectral display will be centered on the peak position, with a width equal to a value specified in the Parameter dialog (0.1 ppm by default). The Y axis limits are set to the maximum value for the dataset. The dataset used for the display is that from which the peak was originally picked. It must already be loaded into NMRView.

Adding Peaks

The simplest way to add a peak to the strip plot list is to type in a peakSpecifier into the entry box above the scrolling list box. Each time you enter a peak into the entry box a new window is created in the display panel. To enter a value, type the peakSpecifier into the entry box and hit Enter.

Peaks can be added from a Tcl script using the NvStripsSetPeaks command. This command takes a single argument, which is a list of the peaks that should be in the Strip Plot list. The specified list of peaks will replace the existing list of peaks. For example,

NvStripsSetPeaks "hncoca.0 hnca.5 hncoca.30 hnca.24"

If the NMRView routines for facilitated assignment of CBCA type experiments are used, then the Strip Plot GUI can be used to display the sequence of peaks that compose any Fragment. To do this enter into the entry box

Fragment fragmentNumber atomType

For example

Fragment 3 CA

will display all the CA peaks comprising Fragment 3.

Adjusting Peak Order

To change the position of a peak in the display click on the corresponding entry in the list box and drag the entry to a new position in the list. The Strip Plot will automatically adjust itself to the new order of peaks.

Removing Peaks

To remove a peak from the list, click on the corresponding entry in the list box to highlight it, and then click the DelPeak entry.

Plotting

The Strip Plot can be plotted using the normal NMRView plot commands. Select Misc->Plot from the Spectrum Menu for any of the windows. Use the PlotAll button in the plotting dialog to plot all the displayed strips as they appear in the Strip Plot GUI.