An ironic 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.
The Strip Plot GUI automatically generates strip plots from datasets based on the positions of a series of specified peaks. The above parameter window is used to specify which datasets and peaks should be used along with several other parameters that determine how the spectrum strips are displayed.
Multiple datasets and peak lists can be displayed in the Strip Plot GUI. Each associated pair of dataset and peak list are referred to here as a dataset/peak pair. Regardless of how many dataset/peak pairs are chosen for display, the user must choose a single peaklist to be the Control List. The chemical shifts of the peaks in the Control List are used to determine the display region for each of the individual strip windows.
When only a single dataset/peak pair is to be drawn, the Offset and Row parameters (see below) should be left at the default values of 0. When the Control List is selected, the Display List for the first dataset/peak pair will be set to the same list. The Dataset for this pair will be set to the dataset associated with this particular peak list. If a different dataset and/or peak list is desired use the Select... buttons to bring up a menu of possible choices for these parameters. The dataset used for the display doesn't need to be that from which the peak was originally picked. It is possible to use a peaklist picked in a spectrum different from that used as the dataset in the Strip Plot. The only thing to take into account is that the names of the labels in the peaklist are identical to those used in the dataset and the dataset must be loaded into NMRView prior to starting the Strip Plot tool.
DimX DimY
The maximum number of window strips that are displayed is specified with the MaxWindows parameter. If 0 is specified for this parameter, then the maximum number of windows will be automatically calculated based on the size (in pixels) of the window display area. The X axis limits for each spectral display will be centered on the peak position, with a width equal to a value specified by the Width parameter (0.1 ppm by default). The Y axis limits are set to the maximum value for the dataset.
When more than one set of dataset/peak pairs are to be displayed, the Offset and Row parameters are used to determine in which window strips the data will be displayed. For example, if two dataset/peak pairs are to be drawn and the first one has an Offset of 0, and the second an Offset of 1, the pairs will be drawn in alternating windows. The first dataset/peak pair will appear in windows 0,2,4,... and the second in windows 1,3,5,...
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