Nudging a Segment

Nudge is perhaps the simplest tool to understand, and the one that you will probably use more often than any other, except for Wiggle.

To nudge a protein, left-click on an amino acid, and drag it across the screen. The amino acid will go where you tell it to (in the original interface, you must be in Pull Mode for this to work). The others to which it is attached will also move in ways that depend on their flexibility, their previous position, and the obstacles they encounter along the way.

Nudge will often cause sidechain clashes; these can be fixed using shake or wiggle sidechains. In fact, nudge is rarely used without one or both of these to resolve the sidechain clashes. Only then will a score typically go up.

When using nudge, it will be noticed that the protein has certain highly flexible areas where it tends to bend more often, and others where it bends less often. Nudge is often nearing the limit of its usefulness when many different nudges in different areas of the protein all tend to cause bends in the same place.

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