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Command: bond

bond  atom-spec  [ reasonable  true | false ]

~bond  atom-spec 

bond length  atom-spec  [ length ] [ move  large | small ]

The command bond adds covalent bonds, ~bond deletes them, and bond length reports or modifies the length of a bond, corresponding to the Adjust Bonds section of the Build Structure tool. A bond can also be deleted using its selection context menu or the command delete. See also: build, angle, torsion, combine, pseudobonds, measurements

A bond can only be added between atoms that are in the same atomic model; if they are in separate models, a single combined model needs to be created first. For bond addition between atoms in the same model, all pairwise combinations of the specified atoms that are within reasonable bonding distance can be bonded (reasonable true, default), or all pairwise combinations bonded regardless of distance (reasonable false). Deletion will include all bonds between the specified atoms, or the bonds themselves may be selected and specified for deletion with the word sel.

The bond length command sets the length of a bond between the two specified atoms to length in Å, or if length is omitted, reports the current value in the Log. The two atoms must already be bonded. Alternatively, a selected bond can be specified directly with the word sel. The move option specifies whether to move the large or small side of the bond (default small, the side with fewer atoms).

UCSF Resource for Biocomputing, Visualization, and Informatics / February 2022