Rotate
rotate can be used to rotate the atomic coordinates of a molecular object. Behavior differs depending on whether or not the object parameter is specified.
If object is None, then rotate rotates the atomic coordinates according to the axes and angle for the selection and state provided. All presentation geometries will need to be regenerated to reflect the new atomic coordinates.
If object is set to an object name, then selection and state are ignored and instead of translating the atomic coordinates, the object's representation display matrix is modified. This option is for use in animations only.
If this doesn't do what you want, consider Turn.
USAGE
rotate axis, angle [,selection [,state [,camera [,object [,origin]]]]]
ARGUMENTS
axis = x, y, z, or float vector: axis about which to rotate
angle = float: degrees of rotation
selection = string: atoms whose coordinates should be modified {default: all}
state > 0: only the indicated state is modified
state = 0: all states are modified
state = -1: only the current state is modified {default}
camera = 0 or 1: is the axis specific in camera coordinates? {default: 1}
object = string: object name (only if rotating object matrix) {default: None}
origin = float vector: origin of rotateion {default: None}
PYMOL API
cmd.rotate(list-or-string axis, angle=0, string selection = "all", int state = 0,
int camera = 1, string object = None)
EXAMPLES
rotate x, 45, pept rotate [1,1,1], 10, chain A
Electrostatic Map Caveat
If you have an electrostatic map and it's not rotating with the molecule as you expect it to, see the Turn command. Turn moves the camera and thus the protein and map will be changed.