RunAbout is set up to operate in a series of modes as you move through the process of assigning your protein. The first mode "Edit Peaks" is designed to let you rapidly examine your datasets. In particular, before you continue with the process of assignment you want to know whether your spectra are peak picked at appropriate levels and whether they are referenced to a common value so that peaks representing the same information align as closely as possible between the different spectra.
Enter Edit Peaks mode by the choosing the corresponding menu entry under the RunAbout Mode menu. Then switch from the Parameters tab to the Helm tab. The Helm tab, as its name suggests provides tools for navigating through your datasets. As shown in this figure the Helm, when in Edit Peaks mode shows the Reference Spectrum and provides buttons for navigating through a peak list (typically set to the reference list). As you move to each peak the chemical shift of the HN and N dimension of that peak are used to set the spectrum display of the reference spectrum which will be shown with the proton dimension on the X axis, and the nitrogen dimension on the Y axis. The Z plane will be set to the carbonyl frequency of the peak (if it's an HNCO spectrum. At the same time as the display of the reference spectrum is changed, all the spectra in the main spectrum display window of RunAbout will be updated.
The number of spectra displayed in the main window will depend on what datasets are available. Typically there will be one row of spectra for each atom type (C, CA, CB). The actual atom types available are determined from the peak list patterns specified. The left half of the spectra are for those experiments that (again, according to the peak list patterns) give rise to i-1 (inter-residue) connectivities (like HNCOCA, HNCOCACB, or HNCO). The right half of the spectra are for those experiments that (again, according to the peak list patterns) give rise to i (intra-residue) connectivities (like HNCA, HNCACB, or HNCACO).
Each spectrum may be shown in two orthogonal views. The carbon dimension is always on the Y axis, but the X axis may display the proton or nitrogen dimension. A set of spectra with the proton dimension on the X axis is always shown. Whether or not the N-C views are displayed depends on the setting of the "N Wings On" button in the View tab. Showing the N-C views allows you to discriminate between peaks that are overlapping in the H-C view, but resolvable in the N-C view. Sometimes, especially if your peaks are well resolved, you may prefer to not display the N-C view, so more screen space is available for the H-C view.
You can also use the controls in the View tab to specify which rows of spectra are displayed. You might, for example, temporarilly turn off the display of the carbonyl (C) spectra by deselecting the "c" checkbox in the "Active" column. Also, by default the complete carbon sweep width of all the spectra is displayed. You can specify a range by entering in values to the MinY and MaxY fields, and turn off the Full checkbox for the appropriate row. Whenever you make a change to these settings, click the Refresh button to update the main spectrum display.
You'll probably find it useful to step through most, if not all, of the peaks in the reference list and observe the corresponding spectra. If you notice many peaks that are not picked, or many artifiacts that are picked, you may well want to go back and redo the peak picking at a more appropriate contour level. If there are many reference peaks that are picked at positions of artifacts or noise you may want to repick the whole spectrum at a different contour level. But you can easily delete a few peaks by clicking the Delete (Skull and Crossbones) button to the right of the up/down peak navigation buttons.
Also note how well the peaks are aligned. In each spectrum a vertical black line is drawn at the chemical shift of the reference peak. The peaks that are likely coming from the same aminde proton should line up right on that line. If not, you may need to adjust the referencing of the spectra. Getting your spectra well aligned at this point, will make things work better in later stages, so spend some time getting this right. Tools available for alignment are described in the next section.
Peak lists can be manually or automatically aligned. To align peaks manually step through the peaks in the Helm until you find a set of peaks you want to use for alignment. Choose a spectrum window in the main RunAbout spectrum display and move the black vertical cursor and adjust it till it is centered over the peak that you wish to be aligned to the reference line. Now click the Manual button in the Alignment section of the "Actions" tab. This will adjust the chemical shift referencing of both the dataset and peak list displayed in that window so that the position is adjusted specified by the crosshair is shifted to the reference line position. You'll need to repeat this process for each spectrum that you wish to align, and for both the proton and nitrogen views of each spectrum.
An automatic peak registration procedure can also be used. In the Actions tab click the "Auto" button in the Alignment section. This will take each peak list and compare it to the reference list. A comparison score is calculated by using a bipartite matching algorithm to come up with the optimum matching between reference peaks and the other list. The offset (for HN and N) between the two lists is iterated till it converges to a minimum. The lists should not be dramatically different in alignment before starting.