Table of Contents
A fact about NMR data is that the significant signals can exist in a vast emptiness of noise. Peak picking routines can extract this information into a concentrated set of numerical values, but it remains valuable to have a visual way to represent the essence of the data sets. One way to attain this is to render the data in a series of narrow strips, the coordinates of which are chosen to select only regions of the data that contain signals.
Typically the coordinates for a particular strip are chosen based on the chemical shift values of an individual peak in a peak list obtained by the peak picking procedure. The coordinates along the x axis are chosen to center the peak in the strip, which generally has a predefined width. The y axis coordinates are generally the full plot limits along the corresponding dimension of the spectrum, though a more narrow range may sometimes be chosen. If the strip has more than two dimensions, then the strip is drawn at the dataset planes closest to the chemical shifts of these additional dimensions.
An issue more complicated than establishing the coordinates of the strips, is deciding what order the strips should be drawn in. The simplest procedure is simply to draw them in order of the peaks in the peak list. Generally this results in strips that are ordered by chemical shift value. Often, however, it is more useful to draw the peaks in an order which places related strips adjacent to each other. For example, in an HNCA experiment strips derived from sequential residues might have peaks with the same carbon chemical shifts, and this can be visually displayed if the peaks are drawn with carbon chemical shifts along the y axis of the strip.
This is often more clearly shown, if the strips are alternately chosen from two different, but complementary, datasets. For example, by alternately displaying the HNCA and HNCOCA experiment, the overlap of the CA chemical shift as derived from the intraresidue HNCA, and the interresidue HNCOCA experiment can be displayed. Sequential connectivities could also be visualized by alternately displaying a TOCSY and NOESY experiment.
It should be noted that NMRViewJ provides powerful features for coordinated analysis of spectra with its RunAbout tool (see below), but if one wants to set up an explicit display of a series of strips of one or more datasets as described here, the Strips tool is appropriate. The Strips tool allows for an unlimited number of datasets to be displayed with varying offsets and rows. In this example the Strips Tool is used so that HNCA and HNCACB datasets are displayed in alternate columns of the first row, and HNCO and HNCACO datasets in alternate columns of the second row.
