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Command: distance

distance  atom1   atom2  [ color  color-spec ] [ radius  r ] [ dashes  N ] [ decimalPlaces  N ] [ symbol  true | false ]

distance delete  atom-spec 
– or –
~distance  atom-spec 

distance style  atom-spec  [ color  color-spec ] [ radius  r ] [ dashes  N ] [ decimalPlaces  N ] [ symbol  true | false ] [ setDefaults  true | false ]

distance save  distance-file

The distance command (see also the Distances graphical interface) adds a distance monitor pseudobond between the specified atoms and labels it with the distance. The current distance is also reported in the Log. Although subsequent changes in distance are not logged, distance labels and the values shown in the Distances tool will update automatically. For click-to-measure, see selection context menus and the distance mouse mode . The tape measure mouse mode adds a different type of distance measurement with markers and links (details...). See also: getcrd, color, style, size, label, clashes/contacts, hbonds, crosslinks histogram, select by pseudobond length, measurements

Distance-monitor pseudobonds are added to a model named distances, with properties matching the first monitor in the model unless different values are given. The defaults can be changed in the Distances preferences or by using the distance style command with setDefaults true.

color  color-spec
Color to use for the pseudobonds (initial default gold
radius  r
Radius in Å to use for the pseudobonds (initial default 0.1).
dashes  N
Number of dashes per pseudobond (initial default 9). Only whole numbers are accepted, with 0 indicating solid sticks. Currently, odd numbers are rounded down to give an even number of dashes.
decimalPlaces  N
Number of digits after the decimal point (initial default 3); affects all distance monitors and is instantly saved as the default.
symbol  true | false
Whether to show the angstrom symbol Å (initial default true); affects all distance monitors and is instantly saved as the default. Distances are assumed to be in Å.

The distance delete or ~distance command removes any distance monitors between specified atoms, or if nothing is specified, all distance monitors.

The distance style command changes the style of existing distance monitors, and setDefaults true (default false) indicates saving the specified values in the Distances preferences as defaults for subsequently created monitors.

The distance save command writes all current distance information (sorted from shortest to longest) to a text file with pathname distance-file. The word browse can be substituted for distance-file to raise a file browser window for specifying the name and location interactively.

UCSF Resource for Biocomputing, Visualization, and Informatics / October 2019