The Edit Links mode the real heart of RunAbout. It is where you and the software connect up the clusters in such a way that the peaks can be assigned to protein residues. Older tools, such as NvAssign for NMRView version 5, would help you with your assignments by evaluating “scores” related to the probability that two clusters are “linked”, i.e., represent two sets of atoms in the protein sequence. Runabout goes further by evaluating the probability that a cluster could be associated with a particular amino acid type, examine the clusters already linked, then determine where in the amino acid sequence that grouping is most likely to occur. Moreover, RunAbout uses the scores of neighboring residues to automatically extend assignments through connections of high probability, thus speeding assignment of easily-determined connections.

Begin editing links by selecting “Edit Links” from the “Mode” pulldown menu atop the RunAbout panel:

Figure 11.15. Entering Edit Links mode

Here’s what will show up when the “Helm” panel is active when editing links:

Figure 11.16. The Edit Links Helm display