It's very important to the use of RunAbout that you assign reasonable contour levels to each of your spectra. Whenever RunAbout assigns a dataset to a particular window, it will use that contour level. If it's not set appropriately your likely to see the spectrum displayed at too high or low of a level. The same goes for setting whether negative and positive contours should be displayed. If you’ve already set appropriate display levels in your spectra’s .nv files, you may wish to check them by opening up “Datasets…Datasets Table” and pulling down to the “Appearance” choice in the Mode pulldown. You should see something like this:

Close the window if these levels look OK.

The simplest way to save these display parameters is to draw each spectrum in a window, get it set to look correct, and click the "Save Dataset Preferences" icon at the lower left of the File Tab of the Spectrum Attributes Window. This will save your current contour level, contour colors and contour positive/negative drawing state to a ".par" file.

Prior to starting Runabout, you need to pick your spectra's peaks. If you have a well-defined system, and you have appropriate contour levels stored in th e NVJ .par files, you may be able to pick all the peaks simultaneously using the main toolbar's Datasets...Pick all peaks menu choice.

If this a new protein system, you should pick each spectrum's peaks separately. The most care should be taken with the HNCO peak list, as this will be used as the reference for all other lists. You should manually clean it up to ensure it carries no spurious peaks. Once you have a good HNCO list, pick peaks in the other spectra, but there's no need to be quite as careful about them. You'll be using Runabout to filter out most of your unwanted peaks anyway.

If the levels are OK and you want to pick peaks completely automatically, click on the Main Toolbar, "Datasets...Peak Pick All". You should see something that looks like this in your swkcon window:

Figure 11.1. Peak Pick All - Results

Make sure you have your protein sequence file, described elsewhere in the documentation.