Chimera Commands Index

adjust ( angle | bangle | bondangle )  new-angle   atom-spec

adjust ( length | blength | bondlength )  new-length  [ movingSide smaller | larger ]  atom-spec

The adjust command can be used to change a bond angle (valence angle) or bond length. See also: angle, bond, rotation, Adjust Bonds, Adjust Bond Angles

Keywords can be truncated to unique strings and their case does not matter. An atom-spec indicates all bonds with both endpoints included.

Only one bond angle (keyword angle, synonyms bangle and bondangle) can be changed at a time, so exactly two bonds with one atom in common must be specified. The new-angle is given in degrees. The first bond specified defines which set of atoms should move as the valence angle is changed.

Any number of bond lengths (keyword length, synonyms blength and bondlength) can be changed in a single command to the same new-length in Å. The movingSide option indicates which set of atoms should move as the length of a bond is changed (default smaller).

Technical Note

If a bond angle is changed by some means other than adjust (such as mcopy), the cached value and subsequent changes with adjust may be incorrect. The solution is to clear the cache before resuming use of adjust, with Python:

import BuildStructure
BuildStructure._bondAngleCache = {}