Distance dynamically calculates and displays distances in angstroms between specified pairs of atoms. Atom1 and atom2 can be any two atoms. They can be specified collectively using the word selected, sel, or picked when the current selection contains only the two atoms of interest. The initial distance is reported in the Reply Log; although the display will update continuously, later values are not sent to the Reply Log.
Distance monitors are displayed as pseudobonds and listed in the Distances tool. Color and other aspects of 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 an atom specification or with the keyword all will remove all distance monitors.
Examples:
distance #1:12@CA #0:47@CA- measure distance between alpha carbons in model 1, residue 12 and model 0, residue 47
~distance #1:12@CA #0:47@CA- stop measuring and displaying the distance between the two atoms
See also: findclash, hbonds, crystalcontacts, the PseudoBond Panel