The distance command measures the distance between two items:
Atom-atom distance measurements are monitors, meaning that a pseudobond is drawn between the two atoms and the pseudobond's label will automatically update to reflect any changes in the distance. Updates are not sent to the Reply Log, however. Distance monitors are listed in the Distances tool. Color and other aspects of pseudobond display can be controlled using the distance monitor attributes panel (opened from the PseudoBond Panel or with the Display options... button on the Distances tool).
An individual distance monitor can be removed by using ~distance with specification of the two atoms involved. Using ~distance without any argument or with the keyword all removes all distance monitors.
Other types of distance measurements (atom-object and object-object) are simply reported in the status line in addition to the Reply Log. For distance measurements, axes are treated as finite line segments, while planes are treated as infinite. For atom-plane and centroid-plane distances only, the signed keyword can be supplied to indicate that distances on opposite sides of the plane should be reported with opposite signs.
Examples:
distance :bgc@c1 a4- measure the distance between atom C1 in residue BGC and axis a4
distance signed p2 :313.a@o- measure the signed distance between plane p2 and atom O in residue 313 of chain A
~distance #1:12@CA #0:47@CA- stop monitoring the distance between atom CA of residue 12 in model 1 and atom CA of residue 47 in model 0
See also: findclash, hbonds, crystalcontacts, angle, define