“distance” creates a new distance object between two selections.
distance [name [, selection1 [, selection2 [, cutoff [, mode ]]]]]
name = string: name of the distance object to create
selection1 = string: first atom selection
selection2 = string: second atom selection
cutoff = float: longest distance to show
mode = 0: all interatomic distances
mode = 1: only bond distances
mode = 2: only show polar contact distances
distance mydist, 14/CA, 29/CA distance hbonds, all, all, 3.2, mode=2
The distance wizard makes measuring distances easier than using the “dist” command for real-time operations.
“dist” alone will show distances between selections (pk1) and (pk1), which can be set using the PkAt mouse action (usually CTRL-middle-click).