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.
rotate axis, angle [,selection [,state [,camera [,object [,origin]]]]]
cmd.rotate(list-or-string axis, angle=0, string selection = "all", int state = 0, int camera = 1, string object = None)
rotate x, 45, pept
if state = 0, then only visible state(s) are affected. if state = -1, then all states are affected.