Start Runabout by clicking on the Main Toolbar "Analysis...RunAbout". You'll then see the main RunAbout window:

Figure 11.2. Runabout Main Panel - initial

It will help to load some data before trying to orient yourself with the RunAbout window. In Runabout's Parameters panel (), click "Guess Lists". If your peaklists are eponymously named for their spectrum type, you should see:

Figure 11.3. Peak Lists

If you've named your lists in a way that doesn't match up with the canonical names, then select them manually. For each list you want ot use, select the type of peak list in the combobox at the left side of each peak list row. Then in the central section of each row choose the actual peak list that corresponds to that type.

RunAbout uses one list as a reference peak list. Typically this will be the hnco (or hsqc if you don't have an hnco). The reference list is selected as the first entry in the Peak List section (labeled RefList).

Much of RunAbout’s analysis concerns matching up chemical shifts in different experiments to determine whether they represent the same resonance. Some error is expected in this process, and the bottom of this Parameters panel is where you can set the tolerances that compensate for this error. The default values, 0.05 (H), 0.2 (N), and 0.6 (C) are pretty good, but you can change them here if you wish. Clicking the Set button will set the tolerances for all the backbone lists to the specified values. You can also have RunAbout calculate appropriate tolerances automatically. Click "Auto" in the Tolerances section of the RunAbout Parameter tab. This will calculate the median line width for each dimension of each peak list and set the tolerance to that value. The underlying code accepts a scale parameter (0.5 would set the tolerance to half the median line width). At present the scale is set to 1.0.

Details of RunAbout's peak list patterns

Next to each peak list, there's a circular "i" button. Clicking it reveals the information RunAbout expects to see in each peak list. This is editable, so if you'd like to add an experiment type, you can edit its expected information here. Here are the informational entries for each of these peak lists:

Figure 11.4. Details of patterns expected for different peak lists

Consider the hnca and hncacb lists as examples. RunAbout expects the hnca to exhibit peaks with 1H and 15N chemical shifts from the amide of residue i, and two 13Cα resonances, one from residue i-1 and one from residue i. The pattern for the hncacb experiment indicates extra information specifying that negative peaks should be interpreted as corresponding to beta carbons.