Chimera Commands Index

distance [ signed ] item1 item2

~distance [ atom1 atom2 ]

~distance all

The distance command measures the distance between two items:

Any specification that gives the proper number of items can be used, including the word selected, sel, or picked to indicate the current selection of atoms and/or objects. Otherwise, objects can be specified by ID as shown in the Axes/Planes/Centroids table. The distance is shown temporarily in the status line and recorded in the Reply Log.

See also: findclash, hbonds, crystalcontacts, angle, define, measure distance, RR Distance Maps

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. The Distances tool lists the current distance monitors and allows setting default distance formatting and depiction options. These settings are stored in a user's preferences file.

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.


distance :bgc@c1 a4
- measure the distance between atom C1 in residue BGC and axis a4
distance c1 c2
- measure the distance between centroid c1 and centroid c2
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