The rotation command activates a torsion (makes a bond rotatable) or adjusts a previously activated torsion (rotates the bond). Active torsions are listed in Adjust Torsions and can also be controlled with that tool. See the video mini-example. See also: angle, adjust, ramachandran, roll, turn, movie-related commands
The command ~rotation freezes a bond in its current position and makes it no longer rotatable.
When atom1 and atom2 are specified, rotation makes the bond between them rotatable. If rot-id is not supplied, the next available integer will be used. The order in which the atoms are specified is not important. If the two atoms (only) are selected, they can be specified collectively with the word selected, sel, or picked. The two atoms must be bonded, and the bond cannot be terminal (not attached to further atoms on either end) or part of a ring. Two rotations cannot affect a common set of atoms unless one affected set is a complete subset of the other. That is, rotations must be properly nested. The ability to activate a rotation does not imply that the bond is freely rotatable in the chemical sense; for example, it could be a double bond. By default, the smaller group of of atoms will move during bond rotation while the larger group remains fixed. The reverse keyword indicates the larger group should move instead. This keyword can only be specified at the time of activation, but an already active torsion can be reversed using the Adjust Torsions dialog.
An already active torsion can be adjusted by specifying its rot-id along with the angle of change in degrees. The rotation can be performed repeatedly for a specified number of frames (default 1).
rotation 2 :16.b@ca,cb- activate a rotation with ID number 2 around the CA-CB bond of residue 16 in chain B
rotation 2 –40- adjust rotation 2 by –40°
rotation #0:1@c:2@n- activate a rotation around the bond between C in residue 1 and N in residue 2 of model 0