“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).

cmd.distance | commands