A chief reason you should be interested in the number of peaks to expect when reviewing a RunAbout cluster is that RunAbout can automatically “trim” clusters down to this size automatically. For instance, if a cluster contains 15 peaks, which is clearly too many, you can cut out the least likely members by clicking the “Trim” button in the left-hand portion of the Helm panel.
In general, the best way to edit your clusters will simply by to scroll through each cluster, check out the alignment of the member peaks, and assess the validity of the number of peaks in the cluster. Clusters with more than expected peaks surely have something that needs fixing, and clusters with fewer than expected peaks should be investigated for overlap.
To create a new cluster from peaks already picked, simply move peaks from the left-hand list of peaks corresponding to the cluster of interest to the right-hand list, which always starts out empty. To move a peak from the left panel to the right in the Helm panel, simply click the name of the peak (e.g., hncacb.45). Likewise, clicking on a peak’s name in the right-hand panel moves it back to the left.
You can treat each spectrum display in the right-hand set of spectra just as you would if it were an individual spectrum. RunAbout includes a number of single-letter keys that facilitate this process:
“z” (for “zoom/unzoom”) enables you to make one spectrum occupy the whole panel. Click in the spectrum of interest and type “z”. Once you’re in this mode, you can move peaks individually by clicking on them (which fills them with transparent yellow tint to show they’re active), moving them around, and changing their boundaries.
“t” lets you toggle the identity of a peak between being an (i)–to–(i-1) correlation and an (i)–to–(i) correlation. RunAbout automatically assigns these types to peaks when creating clusters, but will retain these manual edits if you make them. You can tell which type a peak is by which side of the peak its cluster label is on: (i)–to–(i-1) correlations are labeled on the left, and (i)–to–(i) are labeled on the right.
You can check the i/i-1 status of a peak by examining its entry in the peaklist:
The remaining single letter commands are basically self-explanatory: “a” – Add peak – adds a peak pick to the nearest peak when the left mouse button is clicked.
“d” – Delete peak – deletes the nearest picked peak when the left mouse button is clicked.
“s” – Swap peak cluster
Special Features Neighbor: Clicking the “Neighbor” button will bring to the right-hand panel the cluster nearest to the cluster you’re editing. This will facilitate resolution of some overlap problems, where some peaks are initially assigned to one cluster but really belong in another one nearby.
‘Split” ‘Relink” is the button you MUST click after you’ve adjusted cluster membership. The establishes the new set of links between peaks that constitute the cluster.